Sheppard gets bitten by a Wraith-like bug and is dying. While the puddle jumper returns, it gets stuck in the Stargate. There's 38 minutes to find a solution.

There's suspicion of a Wraith collaborator and some of the team suspect the Athosians. Ford and Sheppard find land on Atlantis' planet.

Two hurricanes are approaching Atlantis and an evacuation is necessary. The leader of the planet taking them in tells the Genii about the situation.

A team of scientists, including McKay, Zelenka and Ford, are exposed to a deadly virus. Sheppard goes after one of the scientists trying to escape.

It's Elizabeth's birthday and she gets a very special gift: a woman who has been in stasis in an Atlantis' laboratory for 10,000 years and is actually herself.

The team is on Dagan, where they must find key stones to retrieve a ZPM. Zelenka finds out Atlantis has a deep space scanner.

McKay finds a way to send a message to Earth, leaving space for personal messages. Sheppard and Teyla are off to spy on the Wraith fleet approaching Atlantis.

Teyla is haunted by nightmares, leaving her agitated. After seeing a psychologist, an old Athosian woman tells her a secret about her ability to sense the Wraith.

McKay and Zelenka come up with a plan to repair the Ancients' weapon satellite. Bates and Teyla get into a fight. He is found unconscious and badly injured shortly afterwards.

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 and the two hive ships are destroyed. Atlantis seems saved, then Zelenka detects 12 more ships. Ford seems changed after a fall in the water.

McKay, Sheppard, Beckett and Weir are on the Daedalus. McKay finds a Wraith virus that is infecting ship systems and sending a signal to the Wraith.

After an attempt to retrieve McKay and Lt. Laura Cadman from the memory banks of a Wraith dart, Cadman gets stuck in McKay's mind.

The team discover an Ancient project to create the ultimate power source. McKay thinks he can finish it. Ronon finds out he is not the only surviving Satedan.

The team is captured by Ford and are forced to take the Wraith enzyme. Ford has a plan.

Sheppard's interrogation is suddenly aborted. Teyla senses another hive ship has arrived. Meanwhile McKay tries to convince his guard to call in help.

The Trust, a Goa'uld terrorist organization, has planted a bomb in Atlantis.

McKay and a pilot crash with a puddle jumper into the ocean on Atlantis. They start to sink.

Atlantis helps with repairing an Ancient shield generator on Taranis. They discover the Taranians are in possession of an Ancient warship.

The 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.

Fallen 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.

Sheppard 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.

The 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.

Rodney's sister is brought to Atlantis to make use of one of her theories.

A device that creates hallucinations affects the team off-world.

The Atlantis expedition must turn to an old friend for help as the Asurans prepare to invade the city.

Teyla witnesses what appear to be an Ancient apparitions, which soon other people start to see.

When 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.

The 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.

With 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.

The Atlantis team finds an Ancient underwater research facility and puts a team together to check it out.

After 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.

With 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.

The 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.

While 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?

While 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.

Rodney 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.

When McKay's sister Jeanie is kidnapped, the team returns to Earth to find her.

When what appears to be a satellite crashes into Atlantis, the team becomes aware of strange behaviour on the base.

The Atlantis team decides to attack the numerous ships of the Replicators, with the help of uneasy alliances.

A transmission from space leads the team to the discovery of a breeding ground for Wraith soldiers.

The 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.

After 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.

Dr. 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.

An empty Daedalus is found orbiting the planet. The team goes to check it out and they are transported to an alternate universe.

A 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.

Rodney is infected with a deadly illness known as "second childhood" which diminishes his mind capabilities and makes him lose his memory gradually.

Dr. 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.

The 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.

Sheppard 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.

When 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.

Radek 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.

An 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?

The killings of a Wraith in Las Vegas are investigated by Detective John Sheppard - who knows nothing about life-sucking aliens from another galaxy.

A 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.

The 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.

The Trust, a Goa'uld terrorist organization, has planted a bomb in Atlantis.

Dr. 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.

With 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.

The team discover an Ancient project to create the ultimate power source. McKay thinks he can finish it. Ronon finds out he is not the only surviving Satedan.

McKay and a pilot crash with a puddle jumper into the ocean on Atlantis. They start to sink.

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.

There's suspicion of a Wraith collaborator and some of the team suspect the Athosians. Ford and Sheppard find land on Atlantis' planet.

A 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.

An 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?