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Todd informs Atlantis that a rogue Wraith has acquired several Z.P.M.'s to power a formidable new Hive ship. When the Daedalus engages it in battle but is unable to defeat it, the team gets a message indicating it is headed to Earth.

In the city of Las Vegas, Detective John Sheppard must solve the case of a long string of unusual murders.

Dr. Keller's body is taken over by a cunning thief, who uses the situation to try and acquire advanced technology from Atlantis.

Sheppard and Lorne investigate a Wraith Hive Ship that has been infected with a strange disease.

McKay returns to Earth to witness the unveiling of his rival's latest breakthrough.

While exploring the mainland of Atlantis' planet, Sheppard is captured by a foe believed to be long dead.

Michael besieges Atlantis in an attempt to kidnap Teyla's infant child.

Sheppard's team is put on trial for crimes against the Pegasus Galaxy, and Woolsey must defend them.

Sheppard and his team try to evacuate a group of Michael's test subjects before the Wraith find and destroy them.

When Daniel Jackson and McKay are trapped in an Ancients lab, Sheppard and the others must get there before Todd the Wraith does.

Daniel Jackson arrives on Atlantis on a research mission to locate Janus' laboratory. However, its discovery triggers off an alien invasion and the possible destruction of the Wraith.

Ronon and McKay have to find a kidnapped Keller, who is abducted to help a village threatened by the Wraith. However, they soon discover that the kidnapper is a Runner.

The Atlantis team is forced to ally with their Wraith contact again when he negotiates an alliance with another Hive.

While investigating one of Michael's facilities, a hybrid creature attacks Sheppard and Beckett.

McKay starts to suffer from the onset of senility to an Alzheimer's-like disease.

When Sheppard's team returns from a mission, a strange electrical surge spreads from their Jumper to Atlantis' systems. It spreads, and the team soon discovers that an old teammate is responsible.

The team is sent through a series of deadly alternate realities caused by a drive malfunction aboard a mysterious duplicate Daedalus, in which they encounter sinister alien lifeforms, a searing sun, and a space battle for Atlantis.

Tyre, Ronon's former Satedan comrade, captures Ronon and turns him over to the Wraith. As the Wraith drain Ronon in an attempt to turn him into a Wraith worshiper, the Atlantis team struggle to find their comrade. Meanwhile Teyla reconsiders her role on the team after the birth of her child.

The Atlantis team is under a quarantine after Dr. Keller is incapacitated by an alien organism, and a recently revived Dr. Beckett is put in charge of the investigation.

In the aftermath of the self-destruct of Michael's compound, Sam leads a team to rescue the survivors. Sheppard, Ronon and McKay must then rescue Teyla from Michael's cruiser as she goes into labor.

Sheppard returns from a mission to find Atlantis abandoned and high and dry on a sand dune thousands of years after his last search for Teyla, but all maybe set right after seeing a hologram of an aged Dr. McKay.

Teyla manages to find some of her missing Athosians... captured by Michael. Also, the Atlantis crew is surprised when Beckett returns.

A deadly disease spreads throughout the Pegasus Galaxy, while Teyla tries to locate her son's father as she travels with Sheppard who's mission uncovers an unexpected find.

When Ronon undergoes a briefing by the IOA, Sam has Teal'c come in to help him. Meanwhile, the Wraith discover the Midway Station.

Rodney, Sam, and Dr. Keller end up trapped in an underground chamber with no means of escape and no one knowing where they are.

Upon learning his father has passed away, Col. Sheppard returns to Earth to attend the funeral. However, Col. Sheppard, along with Ronon who returned along with him, get sidetracked by news that an offshoot group of the Henry Wallace Corp. has created a replicator on Earth, and that the replicator has escaped from the lab.

Sheppard must at the same time deal with his younger brother who thinks his return after more than four years is just to get all his father’s inheritance.

Plus, Sheppard is put in a position where he must ask his ex-wife for a favor that might cost her her job.

Sheppard and McKay escort a young princess on a rite of passage and come upon the queen-to-be's enemies.

An alarm starts a quarantine lockdown, causing members of the Atlantis team to be trapped in various areas of the city, including Rodney being stuck in the botany lab with Katie Brown.

In the aftermath of the Replicator Homeworld destruction, the team discovers an abandoned Hive Ship and investigate. Aboard they find information that leads them to an outpost where the Wraith plan to reactivate the system that allowed them to defeat the Ancients.

Now that they have a Replicator tracking unit to detect the enemy ships, the Atlantis team must destroy them once and for all. However, to do so they have to ally with the Wraith... who have their own plans.

A strange drone crashes into Atlantis, heralding a dreadful new predicament when Replicator doubles of the Atlantis team offer to help defend the city from the Wraith.

The Atlantis team responds when Dr. Rodney McKay's sister, Jeanie Miller, is kidnapped while on Earth.

A psychic visitor delivers a dark forecast for the outpost while at Atlantis. Meanwhile, the Wraith propose an alliance to stop the Replicators, which are annihilating inhabited planets to eliminate the Wraith food supply.

Teyla and Dr. Keller discover an abandoned Athosian settlement and a hostile warrior tribe on New Athos.

The crew suffers from amnesia after plant samples from their new home planet unleash a virus that affects everyone except Teyla and Ronon.

Colonel Sheppard is is captured by the nomadic inhabitants of a fleet of spaceships who wish to use him for their own needs.

Lt. Col. Sheppard touches a crystalline entity causing dreams to become reality and dangerous.

Two years since Ronon Dex learned that a small handful of his people escaped the destruction of his home world Sateda the team encounter some of Ronon's own friends and fellow soldiers who for many years he thought they were killed during a mission to attack the Wraith directly.

Sheppard leads the crew on a mission the core of the Replicator home world. Meanwhile, Samantha Carter is in a race against time to locate Atlantis.

Season 4 begins as Dr. Weir clings to life and Dr. McKay tries to save Atlantis, which is badly damaged and lost in space after the Replicator attack.

A failed attack on a Replicator armada forces McKay to follow in the footsteps of the Ancients, millenia before, and take a drastic step to save Atlantis from destruction.

When Atlantis loses contact with people on Taranis, Weir sends Sheppard and team to investigate. At first they find no life signs, but as they investigate further it appears there is at least one life sign deep underground. Their investigation soon leads them to an old foe’s horrific research which could soon alter the balance of power balance in the galaxy, leaving all humans in an even greater peril than from even the Wraith.

While exploring an ancient drilling platform that could provide Atlantis with more power, the team gets cut off from the jumper and there might be a Wraith after them.

It's a typical Sunday in Atlantis and everyone is going about their daily lives. A handsome scientist, Dr. Branton, who is smitten with Dr. Weir is trying to convince her to go to lunch with him. Although Dr. Weir has a personal rule against dating the people under her command, he persuades her to just "have lunch" with him.

During lunch, Dr. Branton kisses Dr. Weir and she becomes attracted to him, but she decides she can't allow anything to come of this; then the control tower reports that there was an explosion and three people are dead and many injured, and it is believed to have been a bomb.

Sheppard’s team discovers a space station filled with humans locked in a transporter module for hundreds of years. They bring two of them out of status, Jamus and Herick, and are told the survivors 'froze" themselves in the hopes of outliving the Wraith who were attacking them. However, an explosion causes the station to fall out of orbit and traps the team throughout the base.

Major Lorne investigates a planet where one civilization has pictures of McKay, and SGA soon realizes it is connected to an Atlantis control room that McKay and Sheppard had found and thought was just a game room. SGA soon realizes the game room was really an experimental Ancient control room which controls the planet. McKay and Sheppard find that their war game has been affecting the real people on the planet for the last few years. Now Sheppard and McKay must convince both sides that their planet’s struggle was a mistake that they both mistakenly caused. However, they soon learn that they may have led these people into all out war with the technology they mistakenly provided.

While trying to find ways to conserve power in Atlantis, Rodney stumbles upon a room that is using large amounts of power. In an attempt to shut it down he gets hit with a beam and starts developing super powers.

Sheppard and his team head to a planet to investigate reports of a "superhero" in hopes this person might help in their struggle with the Wraith. What they find is a person they have had to unfortunately deal with in the past. However, soon after this meeting, an even worse foe turns up when word spreads that Sheppard is on the planet.

When McKay finds his “whale” circling the floating city, strange events begin to occur. Teyla begins to see people that aren’t there. Then Weir begins to see the same people too. Soon everyone begins to see visions of Ancients who appear to be in distress. Can the arrival of McKay’s whale be connected to these visions? Can the visions the team are seeing forebode an impending event? Also, can the team make sense of the weird voices they are hearing during their visions, in order to understand the unknown danger in front of them? McKay’s answer leads to a daring plan by Sheppard that might just possibly save all the biological life on the planet.

Sheppard and his team, along with Weir and Beckett, arrive in the Asuran's city and destroy the Replicators' stargate operations. The team then escapes, and tries to reprogram a Replicator that had been left floating in space, in order to freeze all the Replicators, so they can rescue O'Neill and Woolsey. However, after O'Neill and Woolsey are captured, the team must come up with a plan B. as plan A has failed. The team goes about this new plan and feeds Woolsey misinformation, as they suspect he will be probed by the Replicators. But will this new plan succeed where their original one failed? Time is against them.

While Atlantis and Earth successfully test a “multiple gate” bridge between their two galaxies, the Daedalus detects another ship. When they try to make contact with the ship, the ship drops out of its time dilated hyper-warp. They learn it is a Lantian war ship returning from a long journey, headed back to Atlantis.

When the Lantian crew learns that all their people had all left Atlantis ten thousand years ago, and that they are the only ones that remain, they politely ask the SGA crew evacuate back to Earth. Gen. O’Neill and Richard Woolsey arrive in Atlantis to try to negotiate with the Lantians, but they are reluctantly forced to agree to leave Atlantis, while Ronon and Teyla decide to stay behind in the Pegasus galaxy.

However, the newly found Latians turn out to be overly confident on their ability to control an impending attack by the Asuran Replicators. Gen. O’Neill and Woolsey then become trapped on Atlantis; as Sheppard, Weir and the rest of SGA break rank with the SGC to try to rescue them and defeat the Replicators’ attack on Atlantis.

Dr. McKay can get them back into the heart of Atlantis, but what sort of resistance will they encounter?

When Sheppard leads a team to find another overdue off-world team, they find the team members are all dead, except for their C.O., who is still missing. They’ve all been shot numerous times with their own weapons. They also find the decaying remains of several Genii soldiers, who have also died violent deaths, some months before. When Sheppard’s team try to return to Atlantis with their dead, they find the DHD has been rigged to explode, which leaves them stranded on this dangerous planet. It appears that an unusual device they have found, which is emitting strange EM pulses, may be the cause of the hallucinations they are all starting to have. However, can they fight off these hallucinations which were the cause of their comrades’ deaths, long enough for McKay to figure out how to turn off the mysterious device?

In a strange twist, McKay’s sister, an accomplished scientist and now a “stay at home” mother, may have found the solution to creating new ZPMs with out knowing it. But McKay’ sister, Jeannie, is reluctant to either assist the military, or help out her brother, whom she has not heard from for over four years.

However, once onboard, McKay and Jeannie put her theoretical physics formulae into practice. The problem is the process that will give them a new power source will also produce “dangerous exotic particles.” Jeannie’s theorem could allow for these dangerous exotic particles to be sent instead to a parallel universe; one that the odds are will be uninhabited, hence not endangering this universe.

During the start up test phase, they are surprised to receive the “McKay” from the parallel universe they are targeting. He tells them that the exotic particles being generated, are about to destroy his universe.

The team must find a way to fix this error, which could also endanger their own universe. At the same time, McKay must also put up with the nicer parallel version of himself, and also try to repair the tension that has existed between him and his sister.

In a convoluted plot to regain power over the Genii, former Commander Kolya captures Col. Sheppard, in order to bargain for the capture of the Genii Ladon. Strangely, Sheppard is able to find an ally in the person being used to scare Atlantis into turning over Ladon, that being the Wraith Kolya is allowing to feed on Sheppard every three hours, a Wraith.

Dr. Weir awakens in a psychiatric hospital only to be told her memories of the last two years of her life were false; just a figment of a psychotic episode she has had over the last two days, after collapsing after a treaty negotiation. Even a visit by Gen. O’Neill to tell her that Stargate Command and an off world Atlantis doesn’t really exist, doesn’t convince her. Then, strange events and changes she sees at the hospital cause her even more doubt about if what is going on around her is really real.

Can she discover the truth of her situation, and can the people she thinks are real back in Atlantis; rescue her from this seeming nightmare?

Atlantis discovers one of the Ancients’ abandoned research outposts, that turns out not to be abandoned.
However, they find they have found a Replicator community living in an even greater “Atlantis like" city, part of which also has the capable of space flight. The learn the Replicators have always wanted to emulate the Ancients, and have also wanted to exceed them. However, they want, but can’t duplicate the Ancients’ final step of ascending.

Now the Atlantis team must escape these Replicators, but not before they also extract the knowledge they have to defeat the Wraith.

Ronon and the team visit a friendly planet, only to find it unfriendly to Ronon, as Ronon brought the wrath of the Wraith down upon them, when they took Ronon in years before while he was a runner. The villagers plan to send them to the Wraith as a sacrifice, as the Wraith has promised not to cull them if they do. Ronon is finally able to get the villagers to at least send his friends back to Atlantis.

The team later returns with reinforcements, but Ronon is gone and the village destroyed. Meanwhile, Ronon has been re-implanted with a Wraith tracking device and dropped on the ruins of his home world “Sateda,” with the Wraith chasing him again as a Runner.

Ronon also begins to experience flashbacks to his past on Sateda, and to the earlier Wraith attacks there. Even as the Atlantis team searches for him, Ronon has plans of his own, and a goal he has set to attain for himself, before he can be allowed to be killed by his trackers.

As Sheppard’s team searches for unused gates to build an easier and faster path back to the Milky Way, they happen on a simple agrarian culture on a planet with an unused orbital gate. There the find Lucius, a town folk who seems to be extremely loved by all those around him. When Dr. Beckett later brings Lucius back to Atlantis unannounced, things there become strange too. Lucius seems to be able to control everyone in Atlantis, except for Col. Sheppard, who has had a recent cold.

Sheppard must find a way to overcome Lucius’ control over the crew, before he becomes a target for opposing their new guest.

As the Hive ship arrives above Atlantis, everyone is happy to find that Col. Sheppard and team are in control. However, the Wraith crew, now turned back in to humans using Dr. Becket’s gas, must be dealt with in some way.

Michael, who now has separately been reverted back to his human form, and the reverted Wraith crew, are relocated to an unpopulated planet which lacks even a stargate. Dr. Beckett then refuses to leave the planet until he is sure the former Wraith won’t revert back to their former state, as Col. Sheppard and team plan to leave back for Atlantis.

At the same time, IOA Agent Richard Woolsey travels back to Atlantis with Dr. Weir to evaluate her command there.

Things do not go as planned, and Dr. Beckett's life becomes endangered. Sheppard and his team must take the crippled Hive ship back to try to rescue him, as a second Wraith ship approaches the planet Dr. Beckett was left on.

With the Wraith ships headed for Earth, Sheppard must find a way to rescue Ronon and McKay. Meanwhile, the IOA makes life hard for Dr. Weir.

The Wraith, or at least one Hive ship, knows of Atlantis’ survival. They learn Michael is on the ship, and finally communicate with him. He tells them that too many Wraith awoke to too few humans, and a civil war then broke out amongst the Wraith.

Michael’s faction wants to get a hold of Dr. Beckett’s retro virus in order to fight the other Wraith factions. They say they can survive by feeding on Wraith who have been converted to humans. Although the Atlantis team is reluctant to believe the Wraith’s motives, they must take the risk to help Wraith in killing other Wraith.

Things go horribly wrong, as the SGA finds the Wraith ship has a totally different agenda. Can Atlantis survive this betrayal? Things look dire for Atlantis! After all, they have given away their Wraith killing information, as well as the fact the Wraith know that Atlantis still exists.

With no way out and trapped on a planet with a volcano, it is up to Dr. McKay to find a way to get the team out of there.

A man is being treated by Dr. Beckett who apparently has amnesia. As he slowly recovers his memory, a major secret is revealed. Also, the secret that Atlantis was not destroyed and Teyla’s life both become imperilled.

Ladon, a Genii scientist who was involved with the Genii’s attempt to capture Atlantis (S1E11: The Eye), contacts the SGA team to coerce them into helping him overthrow the Genii government he had been serving. His enticement is a zero point module that he has in his possession. The team decides it is worth risking the uneasy truce between the SGA and the Genii to acquire the ZPM. But, can they trust Ladon to keep his promise? Strangely, the SGA team finds they have their own ace card to play, when things start to go horribly wrong.

To make matters worse, Maj. Lorne has gone missing while on an away mission. Telya and Ronon are sent to try and find out what happened to him.

Two pods are discovered that contain the minds of alien beings, who take control of Weir and Sheppard's bodies to continue their personal war.

Maj. Sheppard’s team travels to another planet in hope of finding an advanced technologic society to fight the Wraith, only to find another agrarian society. However, they do find the planet holds the one thing (well, several things) that they really need for Atlantis!

However, the Lord Chamberlain of the ruler of the planet machinations put Maj. Sheppard and his team in jeopardy. Only McKay can prevent their demise. But his work endangers him, one of the town folk, the team, and the Tower!

Will they survive?

McKay finds himself trapped in a Puddle Jumper which has crashed into the ocean and is sinking to the bottom. Col. Sheppard must not only locate McKay and the sinking missing Jumper before it’s too late, but also must figure out a rescue strategy to reach the Jumper at the depths to which it is sinking.

Atlantis is threatened by a bomb planted by the Goa'uld. Meanwhile, two Wraith cruisers are on course for the ancient city and a saboteur is unmasked.

The team discovers a portal on a distant planet that pulls Sheppard to another world, where he encounters a dangerous creature. Back on the other side, McKay learns troubling news about the portal.

After being captured during a failed attempt to destroy a Wraith hive ship, Ford, Sheppard, Teyla, Ronin, and some of Ford’s team try to figure a way out of their mess. McKay, who was left behind by Ford as insurance, tries to help the situation by taking a large dose the Wraith enzyme. This leads to a miss direction by the Wraith to Sheppard, and a battle between the Daedalus and two, not one, Wraith hive ship. Sheppard has a plan, but will it work before the Wraith destroy him, his team, or the Daedalus?

Ford, who has survived being beamed aboard a Wraith ship, captures Col. Sheppard and his team. Ford has a daring plan to attack and destroy a Wraith Hive ship, and needs Col. Sheppard and McKay’s knowledge and expertise to pull off the plan. Ford now has a following of converts who are also taking the Wraith enzymes, making them super soldiers too. What the Atlantis team doesn’t realize is, Ford has a plan that will require them to help him, or one of them will die. Things then go horribly wrong, leaving the team in a certain death situation. One must wait for part two to see if and how the team can survive Ford and his team and the Wraith!

The Atlantis team discovers a derelict Ancient spacecraft where the crew is in stasis. They attempt to awaken the crew, but find the Wraith have something to say about this. The question is whether the team can extricate themselves from this revival processes, and remove the Wraith from the equation.

The team races to find a cure for the retrovirus that is mutating Sheppard into a Wraith.

Team finds a planet that has had almost no Wraith culling in the last ten years, or since the time a Wraith ship crash there. However, they are told that one or two survivors must still be alive, as occasionally a villager dies in a culling way. Sheppard offers his teams help to kill the last of the Wraith for them, only to discover when they it, it is a young Wraith female, and she is with the villager who has been protecting her, and acting as her father. The team becomes intrigued by this pair when the father says the deaths could not have been from his daughter, as he has invented a drug that blocks a Wraith’s need to cull on humans.

McKay may have found a new and potent source of energy for Atlantis based on unperfected Ancient technology.

While investigating a new planet, the team is ambushed by villagers. However, a strange craft appears, and rescues them. They learn the planet has a thriving and advanced society, despite the Wraith threat. The SGA team learns that they had been attacked by the worst prisoners on the planet. The prison they arrived on is also the location of the planet’s Stargate

The team finds this strange, but when they find out the truth of this conundrum they are conflicted. Things then go horribly wrong as they attempt to return through the prison island’s gate to consult with Dr. Weir.

A technical glitch during their rescue from a Wraith ship forces McKay and Lt. Cadman to coexist inside McKay's body.

Ronon Dex, a fierce survivor of a Wraith attack, may be the team’s only hope in combating the now dangerous, Wraith-infected Ford.

A mysterious intruder has infected the Dadealus' computers with a virus that may allow them to take control of the ship.

As Lt. Aiden Ford recovers from his near-fatal encounter with a Wraith, the team races against time to save the city from an impending Wraith assault.

A new military contingent from Earth is sent to take command of Atlantis and defend it from the impending Wraith attack.

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.

Teyla begins to have vivid nightmares about the Wraith. Soon this starts affecting her duties. She becomes easily distracted, causing Sheppard to order her to see Dr. Heitmeyer. The session leads Teyla to consult an Athosian elder about her past. The information the elder gives her leads the team to investigate a strange planet where Teyla and her father once lived.

What they find there, and what Dr. Beckett subsequently finds out about Tayla through blood tests, shocks the small group, who learn of Teyla’s secret.

McKay figures out how to send a message back to the SGC, prompting the expedition members to film messages for their families.

The team heads to one of the planets on the list of Ancient outposts, and with the help of the planet's inhabitants, they search for the ZPM. However, old foes show up and plan on taking the ZPM for themselves. [Read Recap below]

During a search of the city, the team finds a 10,000 year-old woman in suspended animation. Thinking she is an Ancient, they wake her up. However, she then reveals that she is Elizabeth Weir. [Read Recap below]

When Sheppard and his team are fleeing from the Wraith in a planet's orbit, an energy wave suddenly wipes the enemy out. Thinking the planet has a powerful weapon, the team investigates, finding a civilization untouched by the Wraith and living in perfect health. They then meet Chaya Sar, the planet's High Priestess, who tells them that it wasn't a weapon, but the work of the goddess Athar.

When members of the expedition begin falling victim to a contagious nanite virus capable of causing death within hours, Atlantis goes into an automatic lockdown. [Read Recap below]

After locating an Ancient defense satellite, Sheppard, McKay, and two scientists detect a Wraith distress signal coming from a nearby planet. They investigate but soon become trapped when an unstoppable Wraith prevents them from reaching their Puddle Jumper.

With Weir and McKay held hostage by the Genii, Sheppard must figure out how to both rescue them and save Atlantis before the storm hits.

A devastating storm occurring every twenty or thirty years is detected approaching Atlantis. The city is evacuated while McKay, Weir, and Sheppard initiate a plan to use the storm's lightning to power the shields. However, before they can finish, they are interrupted by the Genii, who plan to take over Atlantis.

After McKay discovers that a mist covering an alien planet can be used as a powerful energy source for the Stargate, the expedition is able to dial back to the SGC. Told that the Prometheus is being outfitted with Asgard hyperdrives capable of quickly returning them to the Pegasus Galaxy, members of the expedition return to Earth. However, their hopes of returning to Atlantis are shattered when they are informed that due to an accident aboard the Prometheus, they can't go back.

Now separated from Atlantis and stuck on Earth, the team finds strange changes in the things they see and encounter there; the friends and people they knew at the SGC are acting differently than expected.

Sheppard begins to suspect what is really going on, but how can he determine if he is correct?

The Atlantis team travel to the planet of the Genii, known by the Athosians to be good traders of food and crops. As Tayla and Ford barter for food with the farmers, Sheppard and McKay stumble on a secret underground research facility, which belies the society’s technological backwardness. The Genii are close to developing atomic bombs to use against the Wraith. After being captured in the secret site, McKay is intrigued, while Sheppard remains skeptical.

Now the team must either forge an alliance with these unlikely allies, or find a way to extricate them selves from being killed by the Genii, now that they know the team knows their secret.

With Beckett's help, a planet's inhabitants create a drug capable of preventing the Wraith from feeding on them. However, they soon discover the devastating side effects it has on both the Wraith and the user.

Shortly after detecting an energy field, the team's Puddle Jumper unexpectedly crashes. As they begin searching for the field's source to shut it down in order to get their Puddle Jumper working again, they run into a village of children that believe that killing themselves when they reach the age of 24 keeps the Wraith away.

The team comes in hot, having encountered the Wraith for the fifth time in nine missions. There’s no longer any doubt: someone in Atlantis spies for the Wraith. Weir convenes a planning meeting that excludes Teyla. She and Lieutenant Ford establish protective zones against sabotage that exclude the Athosians and interview the Athosians one by one. The Athosians become angry at this suggestion that they’re not trusted. Weir and Sheppard must uncover the spy without alienating the allies who know the Pegasus galaxy.

After Sheppard is attacked by a strange, Wraith-like bug, the team heads back to Atlantis through the planet's orbital stargate. However, their Puddle Jumper gets stuck in the gate when the engine nacelles fail to fully retract into the Jumper, leaving them only thirty-eight minutes to get through the Stargate before the wormhole's event horizon closes.

Kids playing a game of hide and seek in the city, accidentally release a strange and apparently malevolent energy force, which threatens all of Atlantis. Meanwhile, Dr. McKay’s experiment with an Ancient personal protection device leads to a threat to his life.

Can the Atlantis team defeat a formless energy alien while trying to also save Dr. McKay from a slow death?

The Wraith have captured many of the Athosians and SGA expedition members, before leaving through the Stargate. Back at Atlantis the shields continue to lose power, due to the limited energy left in the last remaining ZPM. Major Sheppard eventually gets approval to lead a rescue mission to the Wraith’s ship’s location. The rescue team finds almost all the Wraith are in hibernation in the ship and the captured people stored in cocoons or holding cells.

Sheppard must find away to rescue the people, before more Wraith awaken, but he also is faced with making a terrible sacrifice along the way.

After the gate address to the lost city of Atlantis is found, an expedition departs to the Pegasus Galaxy to check it out. Unfortunately, the city is found on the bottom of the ocean floor, and its shields are quickly losing power. In search of a ZPM or a safe place to stay, a team is sent to the planet Athos. They befriend the planet's inhabitants, but evil beings known as the Wraith then arrive.