Episode Index (titles, seasons, and synopses)

Nitcentral's Bulletin Brash Reflections: Stargate - SG-1, Atlantis, etc: Stargate: Atlantis: Episode Index (titles, seasons, and synopses)
Here’s an alphabetical guide to all Atlantis episodes, giving the title, Season and Episode number and a brief synopsis.

For any episode beginning with “The ...” I have ignored that word when putting episodes into alphabetical order, e.g. “The Lost Boys” comes under “L”.
Adrift (S4-E1) As Atlantis drifts lost in space, Rodney and his team try to repair the damage and find out where they are, while Jennifer Keller and her team try to save Elizabeth, who is suffering from swelling on her brain.

Allies (S2-E20) Michael’s hive ship arrives at Atlantis wanting the retrovirus so that they can turn all enemy Wraith into humans and then feed on them.

The Ark (S3-E16) Team Sheppard finds an apparently abandoned moonbase with no breathable atmosphere, so are rather startled when an unconscious man suddenly appears with no breathing aids. They learn that he has just been reintegrated from a storage device which holds in stasis a thousand residents of the planet below. When a second man is reintegrated, the first one learns of the death of his family and takes drastic action which puts everyone in jeopardy.

Aurora (S2-E9) The crew finds an Ancient warship which has been adrift in space for thousands of years, with all its inhabitants in stasis and their minds connected in a virtual environment where they believe that they are living a normal life. John Sheppard enters the virtual environment in an attempt to communicate with them.

Be All My Sins Remember’d (S4-E11) Daedalus and Apollo arrive with new Asgard plasma beam weapons and wipe out a few of the Replicator ships but are unable to make much of a dent in the fleet. When the Replicator ships retreat to their homeworld, the Atlantis team realise that this is the best time to attack them all in one, but they need some help and ally themselves with both the Wraith and the Travellers for an all-out assault.

Before I Sleep (S1-E15) The team finds a stasis pod in an unexplored part of Atlantis which contains an elderly woman who has been there for ten thousand years. What’s even more bizarre is that the woman is Doctor Elizabeth Weir.

Brain Storm (S5-E16) On Earth, Rodney’s rival opens up a space/time bridge to another universe in an attempt to lower temperatures on Earth. The experiment goes wrong and the facility and everyone inside are in danger of freezing.

Broken Ties (S5-E3) Ronon is captured by his former friend, Tyre of Sateda, and turned into a Wraith worshipper.

The Brotherhood (S1-E16) Searching for a ZPM on a planet, the team has to unravel the mysteries of the Brotherhood who hid the module from ill-doers. Unfortunately, the Genii get wind of their search. Meanwhile a Wraith Dart buzzes the city of Atlantis.

Childhood’s End (S1-E6) The team meets a colony of young people who believe that committing suicide at the age of 25 keeps their village protected from the Wraith.

Common Ground (S3-E7) John is captured by Acastus Kolya, who offers to swap him for Ladon Radim who he believes took his rightful place as leader of the Genii. When Elizabeth refuses to agree to the swap, Kolya feeds John to a Wraith. If the Atlantis crew can’t rescue him soon, he will die of old age.

Condemned (S2-E5) The team finds itself on a planet where the criminals of that world are sent to an island to be culled by the Wraith in exchange for the rest of the inhabitants being left alone.

Conversion (S2-E8) Having been scratched by the Wraith girl from Instinct, John Sheppard begins to transform into an insectoid creature.

Coup d’Etat (S2-E17) Ladon of the Genii offers Atlantis a ZPM in exchange for weapons so that he can carry out a coup against Cowen, who he says is about to use nuclear weapons to bring all humans under his leadership.

Critical Mass (S2-E13) Stargate Command learns that the Goa’uld, via The Trust, have planted a bomb in Atlantis. They manage to relay a message via Daedalus, and McKay disconnects the ZPM to prevent anyone dialling Earth and triggering the bomb. Unfortunately, two Wraith cruisers are sent a distress call by the saboteur and head for the city which now can’t cloak itself without the ZPM.

The Daedalus Variations (S5-E4) Daedalus appears unexpectedly above Atlantis, adrift and abandoned. After Team Sheppard boards it, the ship keeps jumping to alternate universes. Can they find their way back to their own universe while avoiding the inevitable catastrophes along the way?

The Defiant One (S1-E12) Sheppard, McKay and a couple of scientists are en route to investigate an Ancient satellite when they pick up a distress signal from a Wraith ship which has crashed on a planet. Despite being there for thousands of years, one of the Wraith is still alive and kicking.

Doppelganger (S4-E4) John is unwittingly infected by an alien entity which transfers itself from person to person, giving each one horrific nightmares.

Duet (S2-E4) McKay and a female lieutenant are swept up by a Wraith Dart which is then shot down before it can escape. Only McKay can be released from the ship but he discovers that Lieutenant Cadman’s mind has been transferred into his.

Echoes (S3-E12) As Rodney gets a visit from the whale that ‘rescued’ him in Grace Under Pressure, people around the city start seeing what appear to be the ghosts of Ancients, while hundreds of whales starting heading towards the city. John and Rodney finally work out why they’re coming and their connection to the ‘ghosts’ – and it could mean an extinction event for the planet.

Enemy at the Gate (S5-E20) The final episode of Stargate Atlantis. The message sent by the Wraith in Vegas reaches our universe. In an unfortunate coincidence, Todd’s Hive ship has finally acclimatised to the ZPMs stolen from the Replicators and – taken over by Todd’s underling – heads for Earth.

Epiphany (S2-E12) A forcefield surrounding a cave on an alien planet pulls John Sheppard inside. The rest of his team can’t reach him and soon discover that time is moving faster on the other side. By the time the team has got back-up from Atlantis and has found a way through a couple of hours later, Sheppard has been living for six months with a group of people who are on the verge of ascension – but their lives are threatened by a strange creature they call The Beast.

The Eye (S1-E11) Following on directly from The Storm, the Genii have control of Atlantis and are threatening to kill McKay and Weir unless Sheppard gives them the explosives that he has hidden. Meanwhile, the hurricane continues to approach and will destroy the city on arrival.

First Contact (S5-E10) Daniel Jackson and Rodney are kidnapped by aliens and forced to reactivate a device which makes Wraith hyperspace windows unstable. Todd captures Daedalus, while the reactivated device destabilises Atlantis’ Stargate’s event horizon and threatens to destroy the city.

First Strike (S3-E20) Earth’s new battlecruiser, Apollo, heads to Asuras to destroy ships which the Replicators are building. The Replicators retaliate by attacking Atlantis with a powerful beam from space. When sinking the city doesn’t stop the beam, Atlantis takes off and and heads for another planet.

The Game (S3-E15) For the last couple of years, John and Rodney have been playing a SIMS-like game that they discovered in a lab on Atlantis. When Lorne and his team discover a planet where the villagers’ country’s flag has Rodney’s face on it, it becomes clear that John and Rodney’s game has been influencing the villagers’ everyday lives.

Ghost in the Machine (S5-E5) An entity invades the city’s computers and eventually reveals that it is the consciousness of Elizabeth Weir who is in the Replicator version of ascension. However, it’s not all it’s cracked up to be and she needs her friends’ help to regain a body.

The Gift (S1-E18) Teyla suffers from disturbing nightmares and is sent to the base’s resident psychiatrist. Eventually it is revealed why only some Athosians can detect the Wraith’s presence, and Teyla agrees to undergo a dangerous method of gleaning information from the Wraith.

Grace Under Pressure (S2-E14) McKay is trapped alone in the rear compartment of a Puddlejumper which is sinking into the ocean. Back at Atlantis, Sheppard and Zelenka struggle to come up with a way of rescuing him, and McKay comes up with a novel way of staving off his loneliness.

Harmony (S4-E14) John and Rodney are asked to escort an alien princess on a pilgrimage. An easy day’s trek through a forest becomes more complicated when the Genii turn up, attempting to kill her.

Hide and Seek (S1-E3) Rodney McKay finds an Ancient device which makes him impervious to any attack. Unfortunately it also won’t let him eat and he’s in danger of starving to death. Meanwhile, Jinto gets lost in the city and accidentally releases an energy being which has been trapped for ten thousand years.

The Hive (S2-E11) Following on from The Lost Boys, Sheppard and his team, along with Aiden Ford, have been captured on a Wraith hiveship. Back on Aiden’s planet, McKay comes up with a drastic way of escaping his guards.

Home (S1-E9) The team finds a planet with an energy source strong enough to dial back to Earth. Several of them return home but soon find that things are not quite right there.

Hot Zone (S1-E13) Checking the city for damage, members of a large team begin to die after suffering identical hallucinations. All of the team will die unless a cure can be found.

Identity (S5-E18) An accident with a piece of Ancient technology transfers the mind of an alien thief into Jennifer’s body, and vice versa.

Infection (S5-E17) Todd’s Hive ship arrives at Atlantis with all the Wraith on board in hibernation. A recording from Todd reveals that he administered Jen’s gene therapy which removed the Wraiths’ need to feed on humans, but then the Wraith began to die from some unknown illness.

Inferno (S2-E19) Team Sheppard visits a planet which has an Ancient control room. Unfortunately the people of that world haven’t realised that their control room is run using energy from a now not-so-dormant supervolcano, and by running the shield continuously they have drawn too much energy and the volcano is about to erupt.

Inquisition (S5-E13) Team Sheppard is captured by a new coalition of worlds in Pegasus and held to trial for their actions in the galaxy.

Instinct (S2-E7) The team finds a planet where a young Wraith girl is being brought up by a human man who says he has found a way of feeding her without a need for her to drain humans. Beckett takes a prototype drug to the planet which may take the insect part out of the Wraith, but the girl takes the drug before it’s anywhere near complete.

The Intruder (S2-E2) Returning from Earth on Daedalus, Atlantis’ senior staff do not have an incident-free journey. A Wraith virus has invaded the ship and begins to take it over.

Irresistible (S3-E3) Team Sheppard meet a man called Lucius who seems to be adored by all his townsfolk. He offers them some medicines and when Carson Beckett goes to the planet to check the medicines over, he quickly falls under Lucius’ spell and brings him back to Atlantis. Soon, everyone but John Sheppard is equally smitten by the man.

Irresponsible (S3-E13) Team Sheppard travels to a planet where a “superhero” is rumoured to live. They find out that it’s none other than Lucius Lavin who now has other means than his herbs to impress the locals. While they’re dealing with his new methods of conning the villagers, a far more dangerous enemy arrives.

The Kindred [parts I and II] (S4-E18 and S4-E19) Teyla begins a search for the Athosians while the Atlantis crew encounter instances of a new plague in the galaxy, apparently caused by a drug similar to that developed by the Hoffans in Poisoning the Well. Teyla is captured by Michael, who has plans for her baby. The rest of Team Sheppard travel to a facility where they make a jaw-dropping discovery. In Part II, the crew discover the truth about Carson Beckett when tests reveal that he is a clone who will die without medical intervention that only Michael can provide. Meanwhile Teyla is reunited with the Athosians who are being held for experimentation by Michael.

The Last Man (S4-E20) A supposedly normal trip through the Stargate throws John forty-eight thousand years into the future where a hologrammatic Rodney awaits him. As they struggle to find a way to keep John alive long enough to await another solar flare which can send him back, Rodney tells him of the terrible events which occurred after his disappearance.

Letters from Pegasus (S1-E17) With three Wraith hive ships approaching, McKay finds a way to briefly dial Earth and send all the information they have gained so far. Members of the crew record messages home to their families. Meanwhile Sheppard and Teyla are trapped on a planet being culled by the Wraith.

Lifeline (S4-E2) With help from Elizabeth and her activated nanites, Team Sheppard raid the Replicator city for a ZPM but then Elizabeth has to endanger her own life and take on Oberoth, the Replicator leader, to help her colleagues carry out the second part of their plan.

The Long Goodbye (S2-E16) Team Sheppard finds two life pods adrift in space. Retrieving one of them, they find a dying elderly woman inside whose consciousness transfers itself into Elizabeth Weir. The woman, Phebus, says that she will only live a short time in Elizabeth and that she believes the other pod may contain her husband, Thalen. She and Elizabeth persuade John Sheppard to take on the man’s consciousness. Only then do the Atlantis team learn that the two people are mortal enemies seeking one last chance to kill each other.

The Lost Boys (S2-E10) Aiden Ford has teamed up with a group of young men who are now all taking the Wraith enzyme. They capture Sheppard and his team, drug everyone apart from Sheppard and force them to join in their plan to destroy a Wraith hiveship.

The Lost Tribe (S5-E11) Following on from First Contact, John has to hand over the coordinates of the planet where Rodney and Daniel are, even though he knows that Todd will destroy the facility on arrival. Daniel finds out who the aliens really are.

McKay and Mrs Miller (S3-E8) Jeanie Miller – Rodney’s sister – writes a physics paper which solves Rodney’s search for an unending power source. Even Rodney and Sam Carter can’t complete the work without Jeanie’s help – but she is a housewife with a four year old daughter and doesn’t want anything to do with the military.

Michael (S2-E18) A man wakes up in the Atlantis Infirmary with amnesia. He is told that he is Lieutenant Michael Kenmore and that he was captured by the Wraith before being rescued. As he tries to come to terms with his memory loss, mostly with the help of Teyla who befriends him, he starts to have disturbing dreams about the Wraith.

Midway (S4-E17) As Teal’c tries to coach Ronon on how to survive an interview with the IOA without killing anybody, Wraith invade the Midway Space Station and then gate to Earth. Ronon and Teal’c follow and have to take on a small army while John and Rodney have to do the same at Midway.

Miller’s Crossing (S4-E9) Rodney’s sister Jeanie is kidnapped by a man who needs her to help him with nanotechnology in order to save his daughter’s life. When Rodney goes back to Earth to try to find her, he is captured too.

The Misbegotten (S3-E2) The team arrives back at Atlantis with its captured hive ship, flown by Michael. Unfortunately, without Michael’s help, McKay can’t get the ship working without finding a new home for the 200 Wraith transformed into humans. An offworld site is found for them and Beckett continues administering the retrovirus to them – but at least one of the new humans is suspicious that all may not be as it seems.

Missing (S4-E7) Teyla and Jennifer go to New Athos only to find that all the Athosians are gone. Their disappearance appears to be explained when the girls find themselves being hunted by a primitive race of cannibals.

No Man’s Land (S3-E1) As the Wraith hive ships head for Earth, they don’t realise that they have an extra passenger – John Sheppard, who has managed to attach his F-302 to the hull of one of the ships and soon finds an unexpected ally.

Outcast (S4-E15) John returns to Earth for his father’s funeral, accompanied by Ronon. His personal time is soon interrupted when a scientist finds him and reveals that her mentor has built a human-form Replicator on Earth and it has escaped from the lab and is at large.

Outsiders (S5-E12) The Wraith arrive at a village harbouring refugees from another planet struck by the Hoffan plague. While Team Sheppard are trying to take the people to safety, someone turns Carson in as a person who can help the Wraith with his knowledge of the toxin.

Phantoms (S3-E9) Searching for a missing team, Team Sheppard find some dead Genii who appear to have killed each other. After finding a cave with a Wraith generator which is sending out an unusual EM pulse, they find their missing team – three of them dead and apparently killed by their leader. Soon, John and Ronon start living out events from their past.

Poisoning the Well (S1-E7) The Hoffans are developing a means of making themselves unpalateable to the Wraith. Carson Beckett helps them finish the inoculation but then finds the terrible price that will be paid by the Hoffans.

The Prodigal (S5-E14) Michael invades the Gateroom of Atlantis in an attempt to steal Teyla’s baby.

Progeny (S3-E5) The expedition finds a race of people who – at long last – really do appear to be Ancients. Team Sheppard and Elizabeth go to the planet to meet them and find that they are living in a much, much larger version of Atlantis, but soon discover (surprise, surprise) that these people are not what they seem.

Quarantine (S4-E13) Just as Rodney is preparing to propose to Katie, the base unexpectedly goes into a full lockdown, trapping the crew in various places with no communications and so no idea of what’s happening.

The Queen (S5-E8) Jennifer comes up with a means of converting Wraith into normal eaters so that they don’t have to feed on humans any more. Todd is interested but doesn’t have the authority to convince the rest of his alliance of the proposal. Teyla has to undergo surgery and masquerade as a Wraith Queen.

The Real World (S3-E6) Elizabeth wakes up in a psychiatric hospital to be told that she collapsed at a treaty negotiation and that her mind has created a fantasy of her travelling through the Stargate and living in the lost city of Atlantis.

Remnants (S5-E15) Richard undergoes an assessment by the I.O.A. Meanwhile, on the mainland, John is attacked by the last person he ever expected to see alive.

The Return [parts 1 and 2] (S3-E10 and S3-E11) Daedalus encounters a warship which turns out to contain a crew of Ancients who have been travelling through space for ten thousand years. They give them a lift back to Atlantis but the Ancients promptly take command of the city and insist that the expedition leaves. As everyone struggles to adjust to a more normal life on Earth, Atlantis comes under attack by Asurans/Replicators. In Part 2, Daedalus heads to Atlantis to destroy it and its Replicator invaders. John and his team also head there to try and rescue Jack O’Neill and Richard Woolsey and take the city back.

Reunion (S4-E3) As Samantha Carter takes over the leadership of Atlantis, Ronon is reunited with three Satedans who want him to join them in hunting and attacking the Wraith.

Rising [parts 1 and 2] (S1-E1 and S1-E2) Stargate Command finally finds a way to dial the Stargate to the lost city of Atlantis in the Pegasus galaxy. A team of explorers travels there and finds that the city is underwater and in imminent danger of flooding. With no way to return to Earth, a team of marines dials to a planet in Pegasus and meets a race of humans called the Athosians, who tell of an enemy called the Wraith who cull humans on a regular basis. In Part 2, the village is attacked by the Wraith and several Athosians and marines are captured. The others return to Atlantis just in time to witness the city rise to the surface of the ocean to save itself from flooding. Major John Sheppard leads a team to attempt to rescue the captives.

Runner (S2-E3) Searching for Lieutenant Ford, the team meets up with Ronon Dex, a man who the Wraith implanted with a tracking device which they use to hunt him wherever he goes. This is the Wraith idea of fun.

Sanctuary (S1-E14) The team finds a planet which is protected from the Wraith by somekinda Ancient device. Investigating, they meet a woman called Chaya who they persuade to go with them to Atlantis in the hope that they can persuade her to allow evacuees to live on her planet.

Sateda (S3-E4) Ronon is captured by villagers who turn him over to the Wraith. Implanted with a new tracking device, Ronon is dumped on his homeworld, Sateda, and hunted again. The rest of the team have to find a way to rescue him.

Search and Rescue (S5-E1) As Atlantis sends a team to search for survivors of the collapse of Michael’s compound, Michael learns of the explosion and heads for the planet. Can Teyla be rescued from his ship before he can escape again?

The Seed (S5-E2) As Woolsey takes command of Atlantis, Jennifer becomes infected with a mass of tendrils which soon threaten to invade the entire base.

The Seer (S4-E8) Teyla’s wish to seek guidance from a seer who may have knowledge of the Athosians’ fate results in him showing the expedition frightening visions of the imminent demise of Atlantis. Meanwhile the Wraith who worked with John in Common Ground wants help stopping the war with the Replicators.

The Shrine (S5-E6) Rodney is infected with a parasite that – over the course of just a couple of weeks – turns him senile.

The Siege [parts 1 and 2] (S1-E19 and S1-E20) McKay and Grodin travel to the Ancient satellite to see if they can get it working in time to attack the approaching Wraith hiveships. Meanwhile Atlantis’ alpha site is attacked by the Wraith. Is Teyla’s new-found mental link giving away their secrets? In Part 2, Atlantis is just about to evacuate when Stargate Command dials in, having just found a ZPM on Earth. A team of marines arrives to help to defend the city, but the Wraith are too numerous to hold off for long.

The Siege part 3 (S2-E1) Daedalus, Earth’s battle cruiser, finally arrives in time to fight off the last two Wraith hiveships, but many more are on the way. The siege of Atlantis could last for years if another means is not found to drive them away. Meanwhile, Lieutenant Ford, who was attacked by a Wraith and injected with an enzyme which makes him stronger and fitter than normal, starts exhibiting disturbing side-effects.

Spoils of War (S4-E12) Team Sheppard pick up a signal from their former Wraith colleague – now nicknamed Todd – and travel to his hive ship only to find it abandoned. Teyla flies the hive to a secret Wraith outpost where they find a Hive Queen breeding a new army of warriors.

The Storm (S1-E10) As a massive super-hurricane approaches Atlantis, the crew have no choice but to search for an alternative planet to evacuate to. The Genii learn of the evacuation and take over the city.

Submersion (S3-E18) A team takes a Puddle Jumper under the ocean to seek out an Ancient drilling station which may be a source of power for the city. They soon learn that they are not alone down there.

Sunday (S3-E17) Everyone on Atlantis is enjoying a rare day off when a massive explosion rocks the base and leads to tragedy.

Suspicion (S1-E5) When several offworld missions are attacked by the Wraith, Atlantis can only conclude that someone is feeding information to the Wraith. The Athosians naturally are the prime suspects.

Tabula Rasa (S4-E6) A bacterial infection makes almost everyone on the base lose their memories.

Tao of Rodney (S3-E14) Rodney is struck by a mysterious energy beam that turns him into a “superhero” with telekinetic powers, the ability to read minds and an even greater intelligence (not to mention an even greater appetite). Of course, this turns out not to be a good thing and unless he can learn to ascend, he will die.

Thirty Eight Minutes (S1-E4) The Puddlejumper gets stuck partway through the Stargate while trying to return to Atlantis. On board, Major Sheppard has a large bug attached to his neck which is leeching him of his life.

This Mortal Coil (S4-E10) Team Sheppard become suspicious when other members of the expedition start acting strangely. They soon learn that they themselves are not who they think they are – they’re human-form Replicators, created by other Replicators who have established an experimental programme to try to learn how to ascend.

The Tower (S2-E15) Team Sheppard meets a group of villagers on a planet who are preparing their tribute of food to the inhabitants of what they call the Tower. The team discovers that the Tower looks startlingly familiar – it looks exactly like the central spire of Atlantis. When John is taken inside the Tower, he finds that it’s identical inside too. It’s another Ancient spaceship – and this one has a fully functioning Control Chair.

Tracker (S5-E9) Visiting a planet to help the villagers with a bout of flu, Jennifer is kidnapped by a Runner who wants her to help an injured little girl he is travelling with. Ronon has to pit his wits against someone as smart as he is to try to track them, and all the while a group of Wraith are also hunting the Runner.

Travelers (S4-E5) John is captured by a race of people who live permanently in spaceships. They have found an abandoned Aurora-class battleship and need someone with the Ancient gene to help them repair and activate the ship.

Trinity (S2-E6) The team finds a planet with an Ancient weapon on it. Despite a scientist being killed during the first test firing, Rodney McKay becomes obsessed with getting the weapon working. On another planet, Dex finds that not all of his people were killed in the Wraith culling.

Trio (S4-E16) Sam, Rodney and Jennifer fall down a hole.

Underground (S1-E8) The team meets with the Genii who seem to be simple farmers until McKay and Sheppard discover an underground cavern where the Genii are developing nuclear weapons to attack the Wraith.

Vegas (S5-E19) In an alt-universe, police detective John Sheppard investigates a spate of murders in the Las Vegas area where the bodies are shrivelled and skeletal and have large wounds in their chest with finger marks around them. He soon finds himself pursuing a tall man with long white hair and a feeding slit in his hand who has a fondness for heavy music and Goth make-up!

Vengeance (S3-E19) Team Sheppard find the Taranan settlement deserted, but in tunnels underneath the area they find a terrifying new – and much larger – form of iratus bug engineered by an old enemy.

Whispers (S5-E7) John, Carson and a team from Atlantis investigate one of Michael’s labs and come under attack from some of his early hybrid experiments.