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.

The team discovers a planet where the Stargate is kept on a prison island to keep the Wraith satisfied. Their magistrate is willing to trade a rare mineral.

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.

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.

Colonel Sheppard's team finds a world where the leader lives in a tower that possesses the power to stop Wraith attacks.

The team discovers two life pods with a dying woman and man in it. Upon opening Weir gets imprinted with the mind of the woman. She asks a special favor.

While Teyla and Ronon investigate the mysterious death of Major Lorne, the Genii Ladon Radim contacts Atlantis. He wants to trade a ZPM for weapons supplies.

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 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.

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.

After a group of people capture and give Ronon to the Wraith, he becomes a runner again, but this time he's left in his home planet, Sateda, where the Stargate has been disabled.

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.

John Sheppard is kidnapped by the Genii and is in the company of a Wraith.

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 team boards a crippled space station to discover people have been preserved there with the hope to outlive their enemy, the Wraith.

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.

After 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.

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.

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.

Having 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.

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.

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.

Keller, Carter and McKay are stranded in an abandoned Genii mine while off-world.

The 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.

A 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.

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.

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.

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.

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.

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.