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- DirectorWilliam WaringStarsBen BrowderAmanda TappingChristopher JudgeOn another planet, Mitchell is placed under arrest for the murder of a scientist.
- DirectorPeter DeLuiseStarsBen BrowderAmanda TappingChristopher JudgeSG-1 returns early from a mission only to realize that they and Gen. Landry aren't on the same page as far as the the mission they've just completed is concerned. The confusion is quickly resolved when the "real" SG-1 returns at the correct time. Dr. Lam examines them all and concludes that they are identical and thinks they might be clones. Sam, however, thinks they may have come from a parallel universe as the result of the black hole they created when they destroyed the Ori beachhead. As more SG-1 teams arrive from other alternate universes, one of them includes Dr. Fraiser and another includes the Tok'ra Martouf. It's left to Sam and Martouf to find a way to send them all home.
- DirectorPeter DeLuiseStarsBen BrowderAmanda TappingChristopher JudgeLeader of the Hak'tyl and their representative on the Jaffa High Council, Ka'lel has fallen in with those who work against a democratic Jaffa nation. Things worsen when she incapacitates and turns a well-spoken brother Jaffa who promoted democracy. Bra'tac comes to President Hayes and SG-1 for help in finding a now missing Teal'c and uncovering the shadowy dealings in the Jaffa High Council. On Earth, Mitchell gets an old friend of his into a hospital where alien-based technology is used; hopefully, the advances they have made will be able to cure what ails him.
- DirectorKen GirottiStarsBen BrowderAmanda TappingChristopher JudgeA contact within the Rand Protectorate comes to Earth with news that the Ori have given his people a superweapon to use against the Caledonian Federation in exchange for their conversion to Origin. SG-1 plans to turn the people from their newfound religion and destroy the superweapon.
- DirectorPeter DeLuiseStarsBen BrowderAmanda TappingChristopher JudgeWhile investigating the source of an addictive corn-like crop, SG-1 becomes involved in a firefight. They are forced to fall back to the gate, but as Daniel is dialing, both the Stargate and the DHD are beamed away.
- DirectorKen GirottiStarsBen BrowderAmanda TappingChristopher JudgeSG-1 is tasked to accompany members of the International Oversight Advisory, including Richard Woolsey, on a tour of the Gamma site. The visitors are suitably impressed but everyone is put in danger when a carnivorous insect escapes from the lab. The base is locked down and no one is allowed to travel through the gate. The bug is linked to the Ori - it's appeared on several planets that they've visited - and Daniel thinks it may be their follow-up to the virus. SG-1 and the IOA visitors take refuge in a cave, but Gen. Landry is left with little choice but to flood the planet with a deadly neurotoxin to destroy the bugs. SG-1 looks for away out before that happens.
- DirectorPeter DeLuiseStarsBen BrowderAmanda TappingChristopher JudgeSam manages to activate an Ancient device they found at the Glastonbury site and she and Mitchell are shifted into a phase that makes them invisible to everyone. Daniel soon figures out just what is going on but Dr. Lee's proposed solution sends Daniel to the same plane as Sam and Mitchell. There he is able to translate information explaining that Merlin had created a weapon against the Ori - and provides a gate address where it can be found. Meanwhile, Teal'c travels to a Jaffa planet that has sent out a distress call. The two events are related.
- DirectorRobert C. CooperStarsBen BrowderAmanda TappingChristopher JudgeUsing the Ancients' communication technology, Vala, who is in the Ori galaxy, contacts the SGC. She tells them that after being sucked into the wormhole she awoke in a bed in a village much like the one she and Daniel had visited when they used the communication stones. The locals think she fell from the sky - a gift from the gods - and befriends the gentle Tomin, a devout follower of the Ori who has a bad leg. Vala has two pieces of information for the SGC: first, she is pregnant though insists that she didn't have sex with anyone; and second, the Ori have been building a fleet of ships and building up its army. Meanwhile, Colonel Chekov advises General Landry that the Russians will not be renewing their working agreement with the United States and will be taking their Stargate.
- DirectorMartin WoodStarsBen BrowderAmanda TappingChristopher JudgeBased on the information Vala gave them, SG-1 travels to the planet where Merlin may have hidden his secret weapon to defeat ascended beings. There they find an appropriately medieval village and learn that Merlin kept a library there. The locals have never been inside owing to a curse on anyone who dares enter, but SG-1 finds a way in. Once inside, they find a secret chamber that may reveal the location of the weapon. The SGC, meanwhile, has located the Ori's Supergate. Sam's attempt to get control of it is too late, and four Ori ships make their way through. In the ensuing battle, much of Earth's fleet is destroyed, and the future of several SGC members is left in doubt.
- DirectorWilliam WaringStarsBen BrowderAmanda TappingChristopher JudgeAs the Ori invasion continues, Vala and Daniel must deal with their leader, Vala's young daughter, who is rapidly aged by the Ori to serve their purposes.
- DirectorAndy MikitaStarsBen BrowderAmanda TappingChristopher JudgeThe team goes off-world and ends up in serious trouble. Meanwhile, Landry is faced with having to decide whether or not Vala can be trusted to remain at the SGC.
- DirectorWilliam WaringStarsBen BrowderAmanda TappingChristopher JudgeWhile Daniel and Vala search for Merlin's anti-Ori weapon in Atlantis' library, Mitchell, McKay and Carter try to to dial the Ori Supergate in the Milky Way.
- DirectorPeter F. WoesteStarsBen BrowderAmanda TappingChristopher JudgeThe SGC is approached by an Al'kesh bomber which lets itself be taken down, so they can capture Ba'al, who offers to exchange the necessary information to find Merlin's weapon for human help to eliminate his clones, which want to kill him. They mistrust his story, as does NID Agent Malcolm Barrett, who, however, fails to take over the investigation. Since the captive might actually be a clone, several missions to different planets retrieve and capture all clones, but which is the real Ba'al, and what are his true intentions?
- DirectorWilliam WaringStarsBen BrowderAmanda TappingChristopher JudgeA mysterious creature targets members of Stargate Command one by one.
- DirectorMartin WoodStarsBen BrowderAmanda TappingChristopher JudgeMartin Lloyd seeks out SG-1 for assistance when his failed TV show based on the real Stargate program becomes a feature film.
- DirectorAndy MikitaStarsBen BrowderAmanda TappingChristopher JudgeSG-1 is caught in the middle of a war after the Jaffa use a powerful weapon to kill 10,000 Ori followers.
- DirectorPeter DeLuiseStarsBen BrowderAmanda TappingChristopher JudgeVala is kidnapped by agents of the Trust who are trying to find an ancient treasure when an accident causes her to forget who she is.
- DirectorWilliam WaringStarsBen BrowderAmanda TappingChristopher JudgeCameron Mitchell must go undercover inside the Lucian Alliance to find the location of the hijacked Odyssey.
- DirectorAndy MikitaStarsBen BrowderAmanda TappingChristopher JudgeDuring their quest for the Sangraal, SG-1 must join forces with their enemy and face a real-life dragon.
- DirectorAndy MikitaStarsBen BrowderAmanda TappingChristopher JudgeThe SG-1 team hadn't counted on a real dragon as a guardian until one flies out, breathing fire. However, Daniel thinks the Sangraal probably is a hologram. They escape, but the dragon follows them outside. Ba'al admits not to know its secret name, while Daniel believes that the name probably holds power over it. While they guess, Cam thinks of luring the dragon to blow it up, but the C4 barely impresses its digestion. Daniel makes it disappear by using Morgan le Fay's name in Ancient, Ganos Lal. They find it had guarded the frozen 'grave' of the realm's arch-magician, Merlin (or rather, Myrrdin). Vala accidentally triggers a mechanism which revives Merlin when she approaches an Ancient repository device. In the meantime, the team is transported to another planet via the obelisk by the gate outside. Sam surmises that the gate and obelisk are programmed to dial automatically every few hours and transport them to a set of planets that are cut off from the rest of the gate system. Unfortunately, they can't dial out to any other planets either while the program is operating. When he comes to, Merlin seems to confuse the team and Ba'al, with Arthurian characters, but once convinced they are on the same side, he goes to work with the Ancient device to create the Sangraal. Merlin dies at the device, wishing them good luck and referring to one last task. Ba'al's stargate programming skills now seem their only chance. Daniel tries the Ancient repository device himself, but is knocked unconscious. Meanwhile, Adria keeps searching for them via the stargate dialing program on different planets- each time a bit quicker- being one planet behind them. While she is searching, the team is once again transported to another planet, minus Merlin's body. Daniel awakens with valuable memories from Merlin and tries to construct the Sangraal using the repository device again, in exhaustingly intense phases, and finds it also gives him telekinetic powers. It also messes with Daniel's mind, having two different personalities and memories present (his own and Merlin's). Before he can finish the work, Sam and Ba'al disengage the dialing device, just as Adria's Ori troops arrive, allowing SG-1 to escape. Adria is able to capture Daniel before he can escape as well.
- DirectorPeter DeLuiseStarsBen BrowderAmanda TappingChristopher JudgeWhen an entire people may suffer the fatal wrath of a Prior of the Ori for not converting, General Landry orders Carter to try out an experimental device based on Merlin's technology to transport their whole village. The test works, but before they can activate it on a sufficiently large scale, an Ori force takes the village, wounds Sam and kills villagers near the Stargate before Vala's very eyes. Her husband, Tomin, captures her but claims to not love her. He is ordered, as punishment for being deceived by her, to re-educate her. Sam and Cam are able to activate the functioning part of the device, so their building is cloaked from the Ori, who threaten the village leaders and discover and arrest Teal'c. Even after the remaining villagers bow in submission, the Prior decides to destroy everyone since he couldn't find Sam, which makes Tomin doubt his faith, inform Vala, and confront the Prior. The villagers want to sacrifice Teal'c, but one leader stops them. Having seen the Prior destroy the village, Tomin sends Vala down, where she sees if Carter had managed, just in time, to get the device working...
- DirectorAndy MikitaStarsBen BrowderAmanda TappingChristopher JudgeDuring a failed experiment, Samantha is transported into a parallel universe where she cloaks Earth to save it from an Ori attack. Getting back to her own universe is not met with sympathy.
- DirectorAndy MikitaStarsBen BrowderAmanda TappingChristopher JudgeDaniel Jackson, who was left behind fighting off Adria while the other SG-1 members escaped through the Stargate, is found working as a Prior: the best in the business, who doesn't need to use any threats to talk people into conversion to Origin. Hoping there is still some of his personality left, the team (plus General Jack O'Neill) kidnaps him. Daniel explains how he temporarily has Merlin's personality and knowledge in himself, and had deliberately allowed Adria to turn him into a Prior, while delaying to finish Merlin's weapon she'd wanted, and hoping to get an Ori ship for Earth's side. But time is running out since the team took unexpectedly long to rescue him. Still, the generals, Carter, and Vala are most reluctant to go along with releasing him and opening the wormhole he needs to bring the weapon through. Even the White House wants to kill Daniel, or at best, keep him in stasis until he is reverted to his human nature by Merlin's genetic manipulation. But then his plan is wasted - unless the others can be trained to do it in his place (so only they are at risk, not the entire galaxy in case Daniel is Adria's Trojan Horse). After giving them the necessary information, Daniel suddenly frees himself while Richard Woolsey is with him and takes control of a space ship after beaming up Jack too, just after the others have undertaken their mission to Adria's lair, where Daniel, about to be genetically reverted, arrives just in time to tip the balance in their favor.
- DirectorPeter DeLuiseStarsBen BrowderAmanda TappingChristopher JudgeSG-1 blows up three transport ships in a row; Netan puts a price on their heads. General Landry grants the team members spare time on Earth. Daniel spends it researching in a library, where he meets a bounty hunter who tries to seduce him, then switches to her handgun... but is taken out by a bus. Sam gives a lecture on Air Force technological progress together with Dr. Bill Lee; a sniper nearly misses, but is taken out with an experimental weapon they'd brought along to demonstrate. Teal'c is injured by surprise at a Jaffa camp and successfully traps the killer to try again. Cam goes to his Kansas high school reunion and Vala succeeds in making him bring her along, pretending to be his accountant and partner. His still sexy former flame he'd believed out of his reach, Amy Vandenberg, is initially scared off by Vala, but, divorced and interested, explains she still has a secret crush on him. Alien bounty hunter Odai Ventrell assumes numerous classmates' appearances to kill him. Vala's failed rescue gets them both captured publicly, so he threatens to kill off reunion guests unless the other SG-1 members take their place, but they trick him using Chimera technology; they hope Netan's failure to eliminate them will rekindle the power struggle and Odai reacts surprisingly.
- DirectorPeter DeLuiseStarsBen BrowderAmanda TappingChristopher JudgeWhen SG-1, minus Carter, investigates a previously unexplored planet expecting to find themselves in a pyramid, they are astounded to find themselves in a museum. Finding a party occurring in the lobby, they decide to leave and make first contact later, but they find that the DHD is a replica and thus incapable of getting them home. They are discovered and believed to be rebels and are forced to take hostages to buy time for their escape.
- DirectorAndy MikitaStarsBen BrowderAmanda TappingChristopher JudgeTeal'c and Bra'tac are among the numerous victims -though only wounded- of several bomb attacks killing 32 men at a summit in the Jaffa settlement of Dar Eshkalon. As soon as physically able, Teal'c swears to avenge them personally, suspecting the honor-less, ambitious warrior Arkad; General Landry refuses to sanction a killing mission without solid proof, but cannot stop Teal'c from going it alone. Bra'tac explains Arkad's sinister past to Daniel, including the possibility of murdering Teal'c's mother. Information from the resistance on another planet indicates Arkad is in league with the Ori and plans to attack Earth. Arkad comes to meet General Landry, offering to help defend Earth against the Ori, denying any part in the bombings, while defending Origin, incriminating a Jaffa sect. SG-1 is now ordered to find and stop at all cost Teal'c, who is using torture. But Teal'c, committed to killing Arkad, reaches his place, but is wounded, captured, and made to duel Arkad after it is confirmed he had killed Teal'c's parents.
- DirectorPeter DeLuiseStarsBen BrowderAmanda TappingChristopher JudgeStargate Command gets a video message from Vala's extremely unreliable father, Jacek, on the planet Robak; he claims to know about the late Arkad's plans to attack and blow up Earth, even about the several cloaked, Naquadah-laden cargo ships in orbit, and offers details in exchange for sanctuary. General Landry asks Dr. Lam to help him resume contact with her mother, Kim, his ex-wife. Even after the cargoes are found and blown up, Vala abhors her dad's entry. The general asks her to go easy on him, realizing that he, too, neglected his daughter because of his career, even if Jacek's neglect was just criminal. When Cam and Daniel go tell Jacek he shouldn't scam people, he tricks them into talking to Vala for him. Vala goes over just for catharsis, telling him she's through picking up the pieces of his tricks, and he certainly keeps scamming - as Daniel also finds - even with Terak, a Jaffa from an escaped cargo ship, who hopes to sell the Naquadah. When they are apprehended, Jacek promises to help track it and override the rigging of the cargo ship. The Jaffa wait for Jacek and Vala, intending to eliminate them now that Terak is gone, but SG-1 saves them. Since there never was an override, Jacek cheerfully flies away alone in the cargo ship, ignoring that his treachery was anticipated: it's a decoy.
- DirectorWilliam WaringStarsBen BrowderAmanda TappingChristopher JudgeVala gambles, wins a cargo ship, but is found cheating; then Adria appears, throws everyone out and claims she has a new Ori fleet and an operational intergalactic Stargate. Vala tells her scary daughter how she helped Daniel, after a dream, reading the mysterious clava thessara-symbol's mystery, which led to a single planet address, where Athena's treasure house must be; after a disastrous visit there, the team refused to follow the next interpretation, fearing it's just a trap set up by Adria, so Vala is declared a security risk, grounded and confined to Area 51, but escapes through the Stargate. Adria takes her along as she hears the team still plans to visit the address, by starship. Upon arrival, they are trapped by SG-1, which, however, finds itself surrounded by lord Ba'al's troops. Ba'al uses the rings to beam up Adria into an electromagnetic cage in his starship. Back on Earth, General Landry worries what damage the two might do together and wants Adria back. Daniel and Sam now show Vala she has been implanted by Galaran technology with fake recollections of her entire adventure 'til the meeting with Adria. Even though she claims that's impossible, Ba'al is confident he can take control over Adria's loyal Ori troops through her- by implanting a symbiote. The team finds Ba'al's Jaffa and clones killed by symbiote poison, except one Jaffa who secretly used tretonin. The team ring-beams from the cloaked Odyssey starship into Ba'al's, shoots him and captures Adria, but back on Earth, she is found to be under the control of his symbiote. Instead of just killing the evil double, they contact the Tok'ra which send Ta'Seem to extract the symbiote and replace it with a Tok'ra one, but Ba'al manages to poison Adria, who has to be put down. Suddenly Adria wakes up, uses mind-power barricading herself in the sick bay with Vala, tells them she needs time to prepare for ascension, as Daniel guesses outside, and succeeds before the team can cut their way in by blow torch. Nobody knows what this will mean for the future, especially as it remains uncertain whether the Ori are still alive. If not, she may have gained all their former powers, and at least one clone of Ba'al still remains.
- DirectorRobert C. CooperStarsBen BrowderAmanda TappingChristopher JudgeGeneral Landry accompanies SG-1 on a mission to collect the knowledge of the Asgard. When the Ori show up, however, Sam is forced to evacuate the crew. Landry and SG-1 stay aboard, but are stuck helpless in a time dilation field for decades.
- DirectorMartin WoodStarsJoe FlaniganTorri HigginsonRachel LuttrellWhile Teyla and Ronon investigate the apparent death of Major Lorne, the Genii Ladon Radim contacts Atlantis. He wants to trade a ZPM for weapons supplies.
- DirectorMartin WoodStarsJoe FlaniganTorri HigginsonRachel LuttrellMichael Kenmore, a new lieutenant, awakes in the infirmary and doesn't remember a thing. The other expedition members are very concerned about his well-being as he seems different.
- DirectorPeter DeLuiseStarsJoe FlaniganTorri HigginsonRachel LuttrellAtlantis helps with repairing an Ancient shield generator on Taranis. They discover the Taranians are in possession of an Ancient warship.
- DirectorAndy MikitaStarsJoe FlaniganTorri HigginsonRachel LuttrellThe hive ship approaching Atlantis is Michael's. He wants a trade: the retrovirus for not revealing the secret of Atlantis and insights on Wraith technology.
- DirectorMartin WoodStarsJoe FlaniganTorri HigginsonRachel LuttrellFallen into the Wraith trap, McKay initially resigns to fatal captivity in a cocoon, but Ronon keeps struggling to attempt escaping, or at least taking some Wraith down with them. Sheppard managed to hide his glider on the very hive ship, seeking a way out, surprised to get radio contact with Michael, who seeks revenge after the ingrate queen has him semi-restrained as 'too human' suspect. While they try to sabotage the hive and maybe escape, the Daedalus and Orion race just in time to fight the two hive ships before they may attack earth. Weir is summoned to SGC for a pointless grilling by the International Oversight Advisory, finding them bureaucrats unable to risk a decision beyond questioning what was already done. So she returns, never mind the career risk compared to a Wraith culling. Sheppard manages to reach the Daedalus and his party comes up with a daring plan to overpower the hive with the weaponized retrovirus, despite bombarded damage compromising even their life-support systems.
- DirectorMartin WoodStarsJoe FlaniganTorri HigginsonRachel LuttrellSheppard and the others are now in control of the one remaining hive ship with most of the Wraith transformed into human form, courtesy of the retrovirus. They do learn something interesting about female Wraiths, however. After they return to Atlantis, the question becomes one of what to do with the Wraiths who are again human, especially Michael who has proved to be quite helpful. Elizabeth Weir meanwhile is surprised to hear that she is to return to Atlantis as the expedition leader. She will be accompanied however by Richard Woolsey who is to review her leadership and make recommendations to the International Oversight Advisory on whether she should be allowed to continue.
- DirectorMartin WoodStarsJoe FlaniganTorri HigginsonRachel LuttrellSheppard and the team continue their visits to new planets. McKay is tired of all these visits and is keen on implementing a series of gates that will allow them to travel from Atlantis to Earth in a mere 30 minutes without using the power of a ZPM or the two weeks it takes them on the Daedalus. He takes a somewhat different tack however when he sees all of the very friendly young women in the village. Their leader, Lucius Lavin, seems to be a very affable sort and has the locals eating out of their hands. He claims to be an apothecary of sorts and have a cure for every disease, which is certainly of interest to Dr. Beckett. Lavin is invited to Atlantis and soon everyone, including Elizabeth Weir and McKay have fallen victim to his charms. It's left to Sheppard to sort it all out.
- DirectorRobert C. CooperStarsJoe FlaniganTorri HigginsonRachel LuttrellAfter a group of people capture Ronon and give him to the Wraith, he becomes a runner again, but this time he's left on his home planet, Sateda, where the Stargate has been disabled.
- DirectorAndy MikitaStarsJoe FlaniganTorri HigginsonRachel LuttrellThe Atlantis expedition encounters a highly advanced race, the Asurans. They initially believe them to be the Ancients. However, this new race is just a new face of an old nemesis.
- DirectorPaul ZillerStarsJoe FlaniganTorri HigginsonRachel LuttrellDr Weir finds herself on Earth where, to everyone else, the Atlantis Expedition was just her delusion.
- DirectorWilliam WaringStarsJoe FlaniganTorri HigginsonRachel LuttrellJohn Sheppard is kidnapped by the Genii and is in the company of a Wraith.
- DirectorMartin WoodStarsJoe FlaniganTorri HigginsonRachel LuttrellRodney's sister is brought to Atlantis to make use of one of her theories.
- DirectorMartin WoodStarsJoe FlaniganTorri HigginsonRachel LuttrellA device that creates hallucinations affects the team off-world.
- DirectorBrad TurnerStarsJoe FlaniganTorri HigginsonRachel LuttrellThe Atlantis expedition must turn to an old friend for help as the Asurans prepare to invade the city.
- DirectorBrad TurnerStarsJoe FlaniganTorri HigginsonRachel LuttrellThe team returns to Atlantis in an attempt to regain control of the city.
- DirectorWilliam WaringStarsJoe FlaniganTorri HigginsonRachel LuttrellTeyla witnesses what appear to be an Ancient apparitions, which soon other people start to see.
- DirectorMartin WoodStarsJoe FlaniganTorri HigginsonRachel LuttrellThe team investigate rumours of an invincible hero off-world, only to find Lucius Lavin again manipulating a hapless village.
- DirectorMartin WoodStarsJoe FlaniganTorri HigginsonRachel LuttrellWhen Rodney uses an Ancient device, he gets special powers, but soon Dr Weir discovers it's a double-handled gift: if he doesn't ascend, he'll die.
- DirectorWilliam WaringStarsJoe FlaniganTorri HigginsonRachel LuttrellThe Atlantis team finds a program in the Atlantis database which throws Mckay and Sheppard into a Simsesque game that could destroy two civilizations in the Pegasus Galaxy.
- DirectorWilliam WaringStarsJoe FlaniganTorri HigginsonRachel LuttrellThe team boards a crippled space station to discover people have been preserved there with the hope to outlive their enemy, the Wraith.
- DirectorWilliam WaringStarsJoe FlaniganTorri HigginsonRachel LuttrellWith everyone having a Sunday off - something recommended by psychologist Dr. Heightmeyer - all of the members of the Atlantis team pursue leisure activities. Rodney McKay and Carson Beckett are scheduled to go fishing; Sheppard decides to teach Ronon Dex about golf; Teyla spends some time in the gym; and Elizabeth Weir has a lunch date with the handsome Mike Branton. Their day off however is interrupted by a powerful explosion near the mess hall killing and injuring several members of the team. McKay thinks he knows the cause of the problem - a device found by two junior members of his team may have turned some of them into walking time bombs by creating explosive tumors in them.
- DirectorBrenton SpencerStarsJoe FlaniganTorri HigginsonRachel LuttrellThe Atlantis team finds an Ancient underwater research facility and puts a team together to check it out.
- DirectorAndy MikitaStarsJoe FlaniganTorri HigginsonRachel LuttrellAfter losing contact with the new Taranin (the people rescued by the Atlantis team when a super volcano threatened to destroy their planet) settlement, Sheppard's team leaves to investigate. Finding the town deserted, they move to investigate an extensive subterranean tunnel system. What they find there holds dark tidings for the entire Pegasus Galaxy.
- DirectorMartin WoodStarsJoe FlaniganTorri HigginsonRachel LuttrellAfter learning the Asurians are building a fleet of ships, Earth sends its newest ship, the Apollo, under the command of Colonel Abe Ellis to initiate a preemptive first strike to stop them from attacking Atlantis or worse, Earth itself.
- DirectorMartin WoodStarsJoe FlaniganAmanda TappingRachel LuttrellWith a damaged ZPM, and diminished hopes of survival, the Atlantis team finds themselves stranded in the middle of empty space with hardly any time before they run out of power completely. Dr. McKay is challenged to the max as he tries to find a way to save Atlantis from its doom. Meanwhile, Dr. Keller races to treat Weir's increasing head injuries, but the only answer she can come up with could have grave results for everyone on board.
- DirectorMartin WoodStarsJoe FlaniganAmanda TappingRachel LuttrellThe Atlantis team, along with Weir and now with the ability to make large hyperspace jumps in only a puddle jumper, must now journey to the replicator home planet to steal one of their many ZPMs to bring the city back to life, and finish the journey to their new planet.
- DirectorWilliam WaringStarsJoe FlaniganAmanda TappingRachel LuttrellWhile on a regular mission, Ronan runs into some Satedan friends from his past. As old emotions start to return, new thoughts come with them, one of which involves leaving Atlantis. But could danger be lurking just around the corner?
- DirectorRobert C. CooperStarsJoe FlaniganAmanda TappingRachel LuttrellWhile exploring a new planet, Sheppard started to watch a strange crystal. He doesn't know why, but he had to touch it. Back on Atlantis, everybody but him started to have some bad nightmares.
- DirectorWilliam WaringStarsJoe FlaniganAmanda TappingRachel LuttrellSheppard is kidnapped by a group of people living in a starship fleet. They were telling him that they were living on these ships for a long time, due to the war with the Wraith. He was forced to help them make an Ancients' ship fly. Sheppard tricked them and flew with the ship, and 3 of the kidnappers.
- DirectorMartin WoodStarsJoe FlaniganAmanda TappingRachel LuttrellRodney McKay awakens in his lab, tied to a chair and with no memory of who or where he is. He did seemingly leave himself a video message telling him to look for Teyla. The problem began some 14 hours before when Dr. Katie Brown returned to Atlantis with plants from a planet she had visited. The plants had been cleared through the normal quarantine procedure but she is soon afflicted with severe headaches and loss of memory, eventually falling into a coma. Memory loss begins to afflict other members of the crew but they soon become distrustful of one another, making conclusions based on false assumptions and a misreading of the situation. Fortunately, there are two members of the team who seem to be immune.
- DirectorAndy MikitaStarsJoe FlaniganAmanda TappingRachel LuttrellTeyla and Dr. Keller go to the Athosians' new planet, where they discover that the Athosians have gone missing. It seems to be the work of a warrior tribe, the Bola Kai.
- DirectorAndy MikitaStarsJoe FlaniganAmanda TappingRachel LuttrellHaving been told by the Genii spy on New Athos that her people were still alive, Teyla asks permission to visit a man named Davos who is a legendary seer and may be able to help her. When they arrive, Dr. Keller realizes that the man is dying. His ability to see the future is real, but the snippets of the future he is able to show them are open to interpretation. John is called back to Atlantis when they receive a message from the Wraith whose life he had previously saved. He offers to work with McKay to fix the nano virus that is now malfunctioning. As if this weren't enough happening, Richard Woolsey arrives from Earth to undertake Samantha Carter's 3 month evaluation.
- DirectorAndy MikitaStarsJoe FlaniganAmanda TappingRachel LuttrellWhen McKay's sister Jeanie is kidnapped, the team returns to Earth to find her.
- DirectorWilliam WaringStarsJoe FlaniganAmanda TappingRachel LuttrellWhen what appears to be a satellite crashes into Atlantis, the team becomes aware of strange behaviour on the base.
- DirectorAndy MikitaStarsJoe FlaniganAmanda TappingRachel LuttrellThe Atlantis team decides to attack the numerous ships of the Replicators, with the help of uneasy alliances.
- DirectorWilliam WaringStarsJoe FlaniganAmanda TappingRachel LuttrellA transmission from space leads the team to the discovery of a breeding ground for Wraith soldiers.
- DirectorMartin WoodStarsJoe FlaniganAmanda TappingRachel LuttrellThe entire city locks down for a false quarantine, leaving people stranded with a decreasing amount of oxygen, while Rodney is unable to reach a computer.
- DirectorWilliam WaringStarsJoe FlaniganAmanda TappingRachel LuttrellSheppard and McKay must escort a prospective queen as part of their diplomatic duties, unaware that an ambush has been set by some familiar enemies.
- DirectorAndy MikitaStarsJoe FlaniganAmanda TappingRachel LuttrellAfter returning to Earth for his father's funeral, John Sheppard discovers the existence of a human form Replicator loose on the population.
- DirectorMartin WoodStarsJoe FlaniganAmanda TappingRachel LuttrellKeller, Carter and McKay are stranded in an abandoned Genii mine while off-world.
- DirectorAndy MikitaStarsJoe FlaniganAmanda TappingRachel LuttrellThe IOA is conducting interviews back on Earth to ensure that any personnel serving on Atlantis (in particular, aliens) are suitable for their roles. The episode opens up with a pregnant Teyla having been interviewed and reporting back to Atlantis. Ronon is next. Col. Carter is unsure about Ronon's ability to handle the IOA's interview and therefore asks Teal'c to come to Atlantis in a coaching capacity for Ronon. After a rocky start to their relationship, Ronon and Teal'c return to Earth, via the series of Stargates and a Midway Station, that McKay had previously designed. The Midway Station between the Milky Way and Pegasus galaxies serves primarily as a place for those traveling between the galaxies to serve a 24 hour quarantine. While Teal'c and Ronon are serving their quarantine in the extremely cramped Midway Station, it is boarded by the Wraith, via the Stargate, with the intention to travel to Stargate Command on Earth. They achieve this objective, but only with Teal'c and Ronon in tow. What ensues is a battle between the Wraith and the duo of Teal'c and Ronon, for control of Stargate Command.
- DirectorPeter F. WoesteStarsJoe FlaniganAmanda TappingRachel LuttrellA plague of sorts is spreading across the Pegasus galaxy and Dr. Keller estimates that hundreds of thousands will die if they don't don't find a way to stop it. Her research shows however that the disease's origin is with the Hoff, who had been working on a way to kill the Wraith. Sheppard and the others think they know who might be spreading the virus and why. Teyla meanwhile believes she is receiving messages from Kanaan, the father of her child. She's getting his messages while sleeping and most think she's just dreaming. She follows the clues he gives her but she is taken prisoner by an old enemy who has very specific plans for her. In their search for Teyla however, Sheppard and McKay find someone completely unexpected.
- DirectorMartin WoodStarsJoe FlaniganAmanda TappingRachel LuttrellSlowly, everyone on Atlantis comes to terms with the sudden re-appearance of Dr. Carson Beckett who, he claims, has been Michael's prisoner for some two years. He tells them what he was doing in Michael's laboratory and they set off to find the kidnapped Teyla. Dr. Keller figures out just how he's come to there at all. Sheppard meanwhile has been using all of his contacts to try and locate Teyla but they come across someone from the past. Teyla in turn has found some of the Athosians alive but they are few in number as a result of Michael's experiments. Michael explains to her just what it is he wants from her as well as his own plans for the future.
- DirectorMartin WoodStarsJoe FlaniganAmanda TappingRachel LuttrellAfter yet another fruitless search for the missing Teyla, Sheppard returns to Atlantis, only to find it deserted. Worse yet, the city isn't just abnormally hot, but the entire ocean has completely dried up, leaving a sandy desert! Sheppard then finds a hologram of an aged Dr. McKay, telling him that a solar flare had sent him 48,000 years into the future. Once he learns the demise of Atlantis and everyone on it, and worse yet that the sun in the solar system is dying and he won't survive there much longer, he and the holographic McKay must find a way to send Sheppard home and potentially change all of this.
- DirectorAndy MikitaStarsJoe FlaniganRachel LuttrellJason MomoaCombat engineers from Atlantis work against the clock to rescue four of their colleagues who are now trapped in the rubble of Michael's medical compound. With Michael en route, they quickly locate McKay and Major Lorne but Sheppard and Ronon are far deeper and their rescue is not assured. When Michael's ship arrives, they decide to try to rescue Teyla who is in labor and close to giving birth. When it's all over, Col. Carter is recalled to Earth for a performance review but Richard Woolsey has some bad news for her.
- DirectorWilliam WaringStarsJoe FlaniganRachel LuttrellJason MomoaDr. Carson Beckett is removed from stasis because he's the only one who can find the antidote to a mysterious virus that has incapacitated base personnel, beginning with Dr. Jennifer Keller.
- DirectorKen GirottiStarsJoe FlaniganRachel LuttrellJason MomoaRonon is abducted by a Wraith who tries to brainwash him.
- DirectorAndy MikitaStarsJoe FlaniganRachel LuttrellJason MomoaAn empty Daedalus is found orbiting the planet. The team goes to check it out and they are transported to an alternate universe.
- DirectorKen GirottiStarsJoe FlaniganRachel LuttrellJason MomoaA group of beings stranded in sub-space seek help from Atlantis to return to normal space. But their outrageous claims and erratic behavior strains the trust of their benefactors and forces a painful solution.
- DirectorAndy MikitaStarsJoe FlaniganRachel LuttrellJason MomoaRodney is infected with a deadly illness known as "second childhood" which diminishes his mind capabilities and makes him lose his memory gradually.
- DirectorWilliam WaringStarsJoe FlaniganRachel LuttrellJason MomoaSheppard and Beckett battle zombie-like, Wraith-engineered mutants with a team of the best and brightest female SG members.
- DirectorBrenton SpencerStarsJoe FlaniganRachel LuttrellJason MomoaTeyla risks her life on a daring mission aboard a wraith hive ship.
- DirectorWilliam WaringStarsJoe FlaniganRachel LuttrellJason MomoaJennifer, Ronon and Rodney find themselves in the middle of a Wraith hunt when Jennifer is kidnapped by a runner, Kiryk, to help him with a humanitarian mission.
- DirectorAndy MikitaStarsJoe FlaniganRachel LuttrellJason MomoaDr. Daniel Jackson comes to Atlantis in search of a lost Atlantian room. The discovery reveals a new race. Daniel and McKay are kidnapped by the new race and are forced to finish a device which may kill the Wraith. Todd feels betrayed and takes the Daedalus.
- DirectorAndy MikitaStarsJoe FlaniganRachel LuttrellJason MomoaThe new race that stole the device, not to mention Rodney and Daniel, turns out to be an old one meaning very old and well known to the human race. With an ancient grudge to settle, they force Rodney to activate the device against the Wraith with a side effect that could kill millions throughout the galaxy. That makes the Wraith mad so they abscond with the Daedalus to retaliate. Once again we lowly humans have to take control of a messy situation to keep the master races from wreaking havoc in the galaxy.
- DirectorWilliam WaringStarsJoe FlaniganRachel LuttrellJason MomoaThe Atlantis team endeavors to thwart Wraith plans to either find a cure for the Hoffan drug (which makes humans deadly to Wraith feeding on them) or exterminate all those infected.
- DirectorBrenton SpencerStarsJoe FlaniganRachel LuttrellJason MomoaSheppard and his team are lured to a planet and are soon put on trial for crimes against the people of the Pegasus galaxy. In flashbacks, the three judge tribunal recounts the indictment against them including the re-awakening of the Wraith and the various missions where at least a few, if not more, innocent bystanders were killed. Sheppard does his best to argue that on balance, fewer were killed by their presence than would have been the case if they had never been there. A least one of the judges is clearly determined to find them guilty while a second seems far more sympathetic. It's left to Richard Woolsey, who has now joined them, to plead the rest of their case. A lawyer by profession, Richard clearly knows how the game is played and focuses on that third judge.
- DirectorAndy MikitaStarsJoe FlaniganRachel LuttrellJason MomoaWhen the power is shut down and most of the inhabitants are locked out of key controls, it is apparent that Atlantis has been taken over by an off-world group, soon identified as Michael and his hybrids. He is after Teyla's newborn child who is key in his quest to gain control of the Pegasus galaxy. While Sheppard and McKay try to get their hands on a jumper to launch an attack, Ronon and others who were taken prisoner by Michael during his initial invasion launch reprisals of their own. When Teyla manages to get away and hide, Michael gives her a simple choice: surrender herself and her child to him or he will use the city's self-destruct mechanism to kill everyone.
- DirectorWilliam WaringStarsJoe FlaniganRachel LuttrellJason MomoaRadek discovers an alien device that Rodney finds holds serious surprises. Sheppard runs into a reincarnated Acastus Kolya who plans to attack Atlantis. An IOC representative arrives to replace Woolsey who receives advice from a mysterious woman.
- DirectorMartin GeroStarsJoe FlaniganRachel LuttrellJason MomoaRodney finally invites Jennifer on a date; to attend a science conference with him. But petty jealousies arise at the conference that have to be suppressed when a proposed solution for global warming has potentially lethal side effects.
- DirectorAndy MikitaStarsJoe FlaniganRachel LuttrellJason MomoaA Wraith cruiser arrives at Atlantis and is strangely uncommunicative.
- DirectorWilliam WaringStarsJoe FlaniganRachel LuttrellJason MomoaAn alien mind takes up residence in Jennifer's body and seems as confused as her colleagues are by her erratic behavior. Which begs the question; where is Jennifer?
- DirectorRobert C. CooperStarsJoe FlaniganRachel LuttrellJason MomoaThe killings of a Wraith in Las Vegas are investigated by Detective John Sheppard - who knows nothing about life-sucking aliens from another galaxy.
- DirectorAndy MikitaStarsJoe FlaniganRachel LuttrellJason MomoaA hive ship turbo-charged with a ZPM has received the Wraith's message from a alternate universe containing the location of Earth. The ship is now heading for Earth.
- DirectorMartin WoodStarsBen BrowderAmanda TappingChristopher JudgeBa'al travels back in time and prevents the Stargate program from being started. SG-1 must somehow restore history.
- DirectorRobert C. CooperStarsBen BrowderAmanda TappingChristopher JudgeSG-1 search for an Ancient artifact called the Ark of Truth to finally defeat the Ori. However, the Ark is in the Ori's galaxy.