A new Stargate team embarks on a dangerous mission to a distant galaxy, where they discover a mythical lost city -- and a deadly new enemy.

Sheppard tries to convince Weir to mount a rescue mission to free Colonel Sumner, Teyla, and the others captured by the Wraith.

The Atlantis base is threatened when the team discovers that an alien entity is in the city. McKay's experiment with alien technology goes awry.

The team finds themselves in mortal danger when their Puddle Jumper ship becomes lodged in the Stargate.

After a series of run-ins with the Wraith, the team begins to suspect their Athosian allies of having a spy in their midst.

Sheppard and the team visit a world where no one is over 24 years old -- because of a ritual suicide practice they believe keeps the Wraith at bay.

The team finds a world whose people are on the brink of a discovery that may make them immune to the Wraith feeding.

Efforts to open trade relations with a species called the Genii turn sour when the team discovers their new "allies" have ulterior motives.

McKay's efforts to harness the energy of an alien planet's atmosphere allows for a return trip to Earth -- but the team may not be able to return to Atlantis.

When a massive storm threatens the city, Atlantis is evacuated -- only to be taken over by the team's newest enemy.

Major Sheppard plays a dangerous game of cat and mouse with soldiers who have seized control of Atlantis and have taken Weir and McKay hostage.

Sheppard's team investigates a downed Wraith ship, and find themselves stuck on a planet with a lone Wraith survivor.

Nearly a third of Atlantis's residents are infected with a deadly virus that causes hallucinations and death, forcing a lockdown of the city.

The team finds a paradise world that would make an ideal sanctuary for those fleeing from the Wraith, but the local inhabitants believe their goddess will not permit it.

A woman is found in suspended animation in Atlantis, and the team is shocked to see that it is Dr. Weir herself, who tells them of her trip 10,000 years into the city's past.

The team searches for a valuable Zero Point Module rumored to be hidden on the planet Dagan -- but their new allies have motives of their own.

With a brief opportunity to send a data transmission to Earth, members of the Atlantis expedition compose video messages home to their loved ones.

Plagued by terrifying nightmares, Teyla begins to recall a time when she and her father were captured by the Wraith and subjected to disturbing experiments.

With a group of Wraith hive ships on the way to Atlantis, the team searches for a place to flee and a way to destroy the city. McKay leads a team to try and activate the Ancients' orbital weapons platform.

All hope seems lost, until Colonel Everett arrives suddenly from Earth. He is determined to defend the city until the arrival of a ZPM, brought by a new ship.

The Daedalus arrives to defend Atlantis from the Wraith onslaught, but it may not be enough when the team discovers that an even larger armada is on the way.

The Daedalus is infected by a Wraith computer virus, while members of the expedition hope to return to Earth.

Sheppard and his team attempt to locate Lieutenant Ford, only to find themselves captives of a former soldier who is being hunted by the Wraith.

A run-in with a Wraith Dart leaves the consciousness of a precocious Atlantis security officer trapped in Dr. McKay's mind.

The Atlantis team finds a culture that lives in relative safety from the Wraith, because they hand over their criminals to the Wraith -- and crash-land in the volatile penal colony.

McKay puts the team at risk when he tries to perfect unfinished Ancient technology that wiped out a civilization. Ronon Dex discovers that he is not the lone survivor from his world.

The team discovers a young Wraith girl who has been raised by a human, and is in hiding from the people of her human village in fear of her life.

Colonel Sheppard begins to undergo a disturbing physical transformation after being exposed to Beckett's anti-Wraith drug.

When the team finds an Ancient warship adrift on the edge of the galaxy, its crew still alive, Colonel Sheppard enters their virtual reality stasis to communicate with them.

The team is captured by the missing Lieutenant Ford, who is now leading a group of young men who are taking the Wraith enzyme -- and who wants the team's help in a suicide attack against a hive ship.

Colonel Sheppard and his team find themselves prisoners of the Wraith following Ford's attack on a hive ship. Dr. McKay goes to great lengths to help them.

Sheppard finds himself on a planet where time passes more rapidly, with no way to contact his team or return to Atlantis.

When an operative of the Trust plants a bomb in Atlantis, the team must find a spy within their own ranks before the Wraith arrive and discover the city.

When Dr. McKay is trapped underwater in a sinking Puddle Jumper, his only chance for survival may be an hallucination of Samantha Carter.

The team finds a world that possesses Ancient defense technology, where Colonel Sheppard finds himself a pawn in the rivalry between the heirs to the throne.

The team discovers two pods that contain the minds of alien beings, who take control of Weir and Sheppard's bodies to continue their personal war.

After a team from Atlantis goes missing, the expedition finds itself in the middle of a Genii coup.

An amnesiac young Lieutenant in Atlantis suffers from disturbing nightmares that he is a Wraith, only to make a shocking discovery about himself.

Sheppard's team meets a civilization about to be destroyed by a super-volcano, and is trapped there when the Stargate is destroyed during the evacuation.

Michael and his Wraith faction arrive at Atlantis to propose an alliance, hoping to use the retrovirus to transform their Wraith enemies into prey.

レイス側の裏切りにより、彼らを人間にする作戦は失敗に終わった。母船は、レトロウィルスを仕掛けるために乗り込んでいたマッケイとロノンを乗せたまま、ハイパースペースに突入。シェパードもそれを追いかける……。一方、地球からの呼び出しを受けたウィアーは、今回の作戦の責任を問われるのだった。

シェパードたちは、母船を奪取して帰還した。しかし、引き連れてきたレイスたちの処遇が問題となる。レイスは人間化しているものの、ウィルスの効果は未知数。アトランティスに置いておくわけにもいかず、結局、別の惑星に移すことになった。医師としての責任を感じたベケットは、惑星にひとり残って経過を観察する。

とある小さな村で、シェパードたちはルシアスという男に出会った。彼は「宇宙で一番賢くて優しい男」として村人から慕われ、特に彼の作った薬はよく効くことで評判だという。しかし、ルシアスはパドルジャンパーをほしがるなど、執拗に交易を迫ってくる。不信感を抱いたシェパードたちは、早々に立ち去るが……？

ある惑星を探索中のシェパードたちは、村人に襲撃される。彼らの狙いは「レイス招き」のロノンだった。かつて“ランナー”としてレイスに追われていたロノンはこの村に逃げ込み、そのせいで村はレイスに襲われた。その後、生き残った村人たちは、ロノンを生け捕りにする約束をレイスと交わしていたのだった。

探査機からの映像をチェックしていると、画面に研究施設らしきものと人が映し出された。友好関係を築くため、ウィアーたちはゲイトをくぐる。ところが、そこにあったのはアトランティスとそっくりの街。出迎えたニアムによると、彼らはエンシェントの子孫であり、レイスとの戦争で意見が分かれて分裂した一派だという。

目覚めたウィアーは、見知らぬ病室にいた。主治医のフレッチャーによると、ここはワシントン郊外にある精神病院で、彼女は国連の条約調停会議のスピーチ中に倒れ、運び込まれたという。フレッチャーはウィアーがアトランティスに駐留していたことを知らず、不審に思ったウィアーはオニール将軍を呼ぶが……？

ジェナイからの情報で向かった惑星で、シェパードはコリヤに捕らえられた。クーデターを狙うコリヤは、シェパードの命と引き替えにラドンの身柄を要求するが、ジェナイの内乱を避けたいウィアーは別の解決策を見出そうとする。するとコリヤは、捕虜のレイスにシェパードの生命を吸わせ、ウィアーに回答を迫るのだった。

自宅で娘と遊んでいたひとりの女性。ふと何かを思いついた彼女は、大がかりな数式を書き始めた。やがて、彼女の家をカーター中佐が訪れる。数式は、人類を救う世紀の大発見だったのだ……。女性の名はジニー・ミラー。マッケイの実の妹であり、結婚して家庭に入る前は兄と研究を競い合うほどの優秀な物理学者だった。

惑星探査に出たレオナルド少佐のチームが消息を絶った。捜索に向かったシェパードたちは、現地で複数の白骨化した遺体を見つける。何らかの理由で、仲間同士で殺し合ったらしい。捜索を続けると、森の中に小さな洞窟があった。その奥からは、レオナルド隊が調査していたらしい謎のエネルギーが発生していた。

アトランティスのエネルギーが枯渇した。地球との行き来は不可能となり、アトランティスと地球との間に中継ステーションが設けられた。ところが、その運用テスト中にエンシェントの戦艦が出現。かつてのレイスとの戦闘で破損し、宇宙をさまよっていたという。ウィアーたちは彼らをアトランティスに招き入れるが……？

アトランティスは、レプリケイターに乗っ取られた。現地にいたオニール将軍とウールジーはレプリケイターたちの目を逃れ、都市内に潜んでいる。一方、シェパードたちは、ランドリー将軍の帰還命令を振り切ってアトランティスへ。オニールと連携してアトランティスを取り戻すべく、作戦を立てる。

テイラは、白いドレスを着た謎の女性が通路を歩いているのを目撃した。女性は意味不明の言葉を発しながら、こちらへ向かってくる。そして、いまにもぶつかりそうになった瞬間、幽霊のごとくテイラの体を通過してしまった。ところが、その光景はテイラにしか見えていないらしい。この不思議な現象の正体とは……？

ある町に英雄がいると聞き、調査にやって来たシェパードたち。しかし、英雄とはルシアスのことだった……。彼はこの町でも人気者だったが、彼の語る武勇伝は嘘ばかりで、得意の薬を使った形跡もない。怪しむシェパードたちを前に、ルシアスは自分の力を見せつける。なんとルシアスは不死身の体になっていたのだ！

節電のため、アトランティス内の不要な装置を止めることになった。その作業中、ある装置の操作盤に触れたマッケイは、装置から発生した謎のパルスに直撃されてしまう。健康診断の結果、体に異常はなかった。しかし、マッケイは遠くの話し声が聞こえたり、念じたことが現実になるなど、次第に超能力を発揮するようになる。

ローン少佐からの報告で、軌道上に複数の人工衛星を浮かべている惑星が発見された。地上の住民の暮らしぶりからは、それほど高度な科学技術を持っているようには感じられない。しかし、驚いたことに、町内に掲げられた国旗にはマッケイの顔がプリントされている。マッケイは、その旗に心当たりがあった……。

シェパードの操縦するシャトルは、墜落寸前だった。その8時間前、彼はマッケイたちと、ある月の地中に作られた古い施設を調査していた。奥にはひとりの男が倒れており、ヘリックと名乗る。かつて彼は仲間たちとともにレイスと戦っていたが、敗色濃厚となり、レイスの転送技術でこの施設に長期保存されていたという。

医師の指示により、アトランティスは一斉休暇に入っていた。この日、シェパードはロノンとゴルフに興じ、ベケットはマッケイを釣りに誘うなど、それぞれの休日を楽しんでいた。しかし、食堂付近で爆発が起き、居合わせたテイラは重傷を負ってしまう。爆発の原因は装置の故障ではなく、爆弾によるものだというが……？

ウィアーたちは、海底の地熱掘削基地を探していた。基地は移動式で探索は難航するものの、稼働させれば無限の動力を得られる可能性もあり、ウィアーは大きな期待を寄せる。基地はやがて発見され、内部の調査が始まった。しかし、レイスの気配を感じたテイラは、その存在を確認するため、レイスとの意識交信を申し出る。

タラニス人と連絡が途絶えてから数ヶ月が経っていた。調査に行ったシェパードたちは、村の地下に生命反応をキャッチする。地下には何かの施設があり、一室には空のマユが残されていた。さらに探索を続けると、タラニス人が大量死しているのが発見される。死者たちの首には傷があり、シェパードはその傷に見覚えがあった。

レプリケイターが船を大量に建造していることが判明した。目標は地球と見られるため、直ちに奇襲作戦が展開されることになった。作戦の指揮を執るのは、地球から来たエリス大佐。核弾頭で船を爆破するという作戦に、ウィアーは中途半端な先制攻撃は危険だと警告する。しかし、エリスは作戦を強引に推し進めていく……。

Floating in deep space with the city's protective shield failing, the team must do all they can to keep Atlantis alive. A radical injury threatens Dr. Weir's life.

Colonel Sheppard and his team embark on a risky mission to steal a Z.P.M. power module from the Replicators -- but must rely on a compromised Dr. Weir to succeed.

When a group of Ronon's people enlist the team's help in raiding a Wraith weapons facility, Ronon reconsiders whether his future lies in Atlantis or with his friends.

During an off-world mission Colonel Sheppard unknowingly becomes host to an alien entity, which infects others in Atlantis and afflicts them with terrifying nightmares.

Colonel Sheppard is captured by the inhabitants of a generational ship and their beautiful leader, who wish to use his ability to use Ancient technology for their own ends.

When a virus causes amnesia in everyone except Teyla and Ronon, the Atlantis team must work together to find a cure before their memories fade entirely.

During a visit to New Athos, Teyla and Dr. Keller find themselves on the run from a primitive tribe of warriors.

The team meets a man with extraordinary prophetic abilities, who gives them a dark prediction about Atlantis's future. The Wraith seek a new alliance with Atlantis in their war with the Replicators.

Rodney McKay goes in search of his sister on Earth after she is kidnapped by the head of a powerful corporation.

A mysterious drone crashes into Atlantis, indicating that the Replicators may have found the city. But when Elizabeth Weir appears, the team realizes that the probe is just a part of a bigger mystery.

With a plan to potentially extinguish the Replicator threat, the Atlantis team must seek an alliance with a fleet of Wraith ships.

The team finds their former Wraith ally's hive ship drifting in space, which leads them to a secret project that could turn the tide of a civil war.

An automated lockdown traps Atlantis personnel in various parts of the city, each of them hoping the others will come to their rescue.

Colonel Sheppard and Dr. McKay must protect a child princess on a pilgrimage before she can become queen, and learn that she has dangerous enemies threatening her life.

While on personal leave on Earth, Sheppard and Ronon learn that scientists have engineered a human-form Replicator -- who is now on the loose.

McKay, Carter, and Keller are trapped in an underground chamber while on an off-world mission, with no apparent means of escape.

Teal'c visits Atlantis to counsel a headstrong Ronon, who is up for review by the I.O.A. But the two must work together when the Wraith invade the Midway space station in order to reach Earth.

As a mysterious new illness sweeps through the Pegasus Galaxy, Teyla is convinced by a vision that the father of her child is trying to communicate with her.

The team is shocked when an old friend, believed to be dead, miraculously returns to them. Teyla plans an escape from Michael's captivity.

Sheppard returns to Atlantis after a mission and finds the city abandoned, all systems dead -- and instead of ocean, sand dunes as far as the eye can see.

Lt. Colonel John Sheppard and his team are trapped under the rubble of Michael's facility in order to rescue Teyla Emmagan. As Colonel Samantha Carter launches a team to rescue the rescuers, little do they know that Michael Kenmore is also searching the planet for the survivors.

When a mysterious alien organism takes Dr. Jennifer Keller as its host, the newly revived Dr. Carson Beckett and the crew desperately search for a serum to save her from the evolving intruder before it can infiltrate Atlantis. In the meantime, Richard Woolsey officially joins the team, having been chosen as Colonel Samantha Carter's replacement to lead the Atlantis expedition.

Ronon Dex is captured by Tyre, who wants to hand him to the Wraith in order to maintain his role in their circle. However, when the deal turns sour, and Tyre is left for dead, the Atlantis expedition persuade him to take back their friend. Meanwhile, The Wraith turn Ronon into a Wraith worshipper.

The Atlantis expedition mysteriously finds the Daedalus, abandoned and drifting in space. When Lt. Colonel John Sheppard's team come to investigate, the ship mysteriously disappears. They soon discover that the ship is actually an alternate Daedalus from a Alternate reality, and the team must find a way back to their Universe or risk being stranded forever in an unfamiliar reality.

While on a mission, Lt. Colonel John Sheppard's team inadvertently brings a mysterious entity to Atlantis. They soon learn that the entity is nothing more than Dr. Elizabeth Weir, who was thought to have been killed after her capture by the Asurans.

緊急の呼び出しを受けて急遽アトランティスへやって来たジニーは、あるビデオを見せられる。映っているのはマッケイ。いつもとは明らかに様子が違い、自分の名前すらうまく思い出せないようだ。実はマッケイは未知の病で余命わずかとなり、家族に最後の別れをさせようとジニーが呼ばれたのだった。

Dr. Carson Beckett is called in to help a team investigating a lab that once belonged to Michael Kenmore. But soon, they realize that a group of experiments that even Michael couldn't control are hellbent on killing the team.

The Atlantis expedition has a plan to remove the Wraith's dependence on feeding to use an experimental gene therapy from Michael's database. However, in order to convince the Primary, the Wraith leader, Teyla Emmagan must pose as a Hive Queen.

Dr. Jennifer Keller is kidnapped by a runner named Kiryk. While Dr. Rodney McKay and Ronon Dex tracks them, Kiryk takes Keller to a seriously injured young girl. She must do it fast, since the Wraith have found him, and are hunting them down.

Dr. Daniel Jackson arrives in Atlantis to investigate a hidden lab left behind by the rogue Ancient scientist Janus. Their discovery has attracted the attention of a mysterious group of aliens, who infiltrate the city. Meanwhile, "Todd" and a delegation arrive on the Daedalus to bring forward Dr. Jennifer Keller's gene therapy.

As Dr. Rodney McKay and Dr. Daniel Jackson is held prisoner by the Vanir, they make a startling discovery about who they really are. Meanwhile, "Todd" and his Wraith hijack the Daedalus to find and destroy those who activated the Attero device. The Travelers arrive and Lt. Colonel John Sheppard must help them get to the planet before "Todd" uncovers a way to discover the device for good, even if it means sacrificing McKay and Jackson's lives to do so.

Dr. Carson Beckett, now a traveling doctor in Pegasus comes across a planet, where some of the villagers are refugees from Balar, a planet infected with the Hoffan drug, and destroyed by the Wraith. However, the Wraith arrive on the planet and gives the village an ultimatum, hand over the Balarians, or face destruction of the entire civilization.

Lt. Colonel John Sheppard's team is invited by the Coalition of Planets in order to form an alliance. However, the team is misled and is faced to stand trial, for their alleged crimes against the Pegasus galaxy. Their best chance of freedom, is the experiences of Richard Woolsey.

Michael Kenmore has infiltrated Atlantis with an army of his Hybrids, and closes off Stargate Operations and the surrounded levels to prevent anyone from taking it back. His plan; take Teyla Emmagan and her child to perfect his Hybrids, and to destroy the base when they're done. Meanwhile, Lt. Colonel John Sheppard, Dr. Rodney McKay and a team try to take back the city before Michael leaves with what he wants.

While being evaluated by the International Oversight Advisory, Richard Woolsey meets a beautiful scientist new to Atlantis, who is not what she appears. Meanwhile, Lt. Colonel John Sheppard is captured and tortured by an enemy he thought he'd killed several years ago: his sworn enemy, Genii Commander Acastus Kolya.

Dr. Rodney McKay reluctantly returns to Earth to witness the triumph of his rival Dr. Malcolm Tunney, but must help shut down a deadly weather device when the new technology goes horribly awry.

After a Wraith Hive Ship shows up over Atlantis transmitting a distress call, Lt. Colonel John Sheppard's team discovers that its crew has been stricken with a disease they helped create.

Dr. Jennifer Keller's body is inadvertently taken over by a cunning thief, Neeva Casol. While Neeva tries to escape Atlantis, Keller finds herself imprisoned with a death sentence on another planet, forcing the team into a race against time to return Keller to her original body before she is put to death.

In the city of Las Vegas in an alternate reality, police Detective John Sheppard investigates a series of bizarre murders where each body appears to have desiccated. He is soon called to Area 51, where Dr. Rodney McKay explains the situation.

少し前、シェパードが約束を守って自由にしたトッドから通信が入った。瀕死だった彼はイレイタス・バグの女王をエサにするという究極の治療に成功し、再びレイス同盟のリーダーに返り咲いたが、部下の裏切りにあいその座を追われたと言う。原因は以前トッドが入手したZPMだった。