4.01 – Adrift

(September 28, 2007) Directed by: Martin Wood

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.

4.02 – Lifeline

(October 5, 2007) Directed by: Martin Wood

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.

4.03 – Reunion

(October 12, 2007) Directed by: William Waring

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?

4.04 – Doppelganger

(October 19, 2007) Directed by: Robert C. Cooper

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.

4.05 – Travelers

(October 26, 2007) Directed by: William Waring

Returning to Atlantis in a puddle jumper after a resupply mission, John Sheppard is abducted and questioned by a group of nomadic space travelers who have no home planet and live perpetually aboard their spacecraft, traveling through the Pegasus galaxy. They have in their possession an Atlantean ship but have been unable to activate the hyperdrive. They’ve kidnapped Sheppard for his gene that they hope will allow them to use the ship to its full capacity. Sheppard isn’t exactly a cooperative prisoner and soon shows them what can be done with the Ancients technology. His efforts to send a signal to his own team however also alerts the Wraith to their presence and he must join forces with his captors if they are to survive.

4.06 – Tabula Rasa

(November 2, 2007) Directed by: Martin Wood

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.

4.07 – Missing

(November 9, 2007) Directed by: Andy Mikita

Teyla and Dr. Keller go to the Athosians’ new planet, where they discover that the Athosians have gone missing. It seems to be the work of a warrior tribe, the Bola Kai.

4.08 – The Seer

(November 16, 2007) Directed by: Andy Mikita

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.

4.09 – Miller’s Crossing

(November 30, 2007) Directed by: Andy Mikita

Rodney McKay is continuing to work on solving the problems with the replicator nano code and finally gives in to Zelenka’s request that he contact his sister Jeannie for help. He sends her an e-mail but that same night, she is kidnapped and taken to a private medical facility where she is expected to use nano technology to save the life of a wealthy industrialist’s daughter. Rodney and others travel to Earth to look into Jeannie’s disappearance but Rodney is soon kidnapped and put to work as well. Rodney and Jeannie think they have found a working solution but when it fails, there is only one solution left to them – they need expert help and the only expert who knows more they do is Todd the Wraith.

4.10 – This Mortal Coil

(December 7, 2007) Directed by: William Waring

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

4.11 – Be All My Sins Remember’d

(January 4, 2008) Directed by: Andy Mikita

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

4.12 – Spoils of War

(January 11, 2008) Directed by: William Waring

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

4.13 – Quarantine

(January 18, 2008) Directed by: Martin Wood

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.

4.14 – Harmony

(January 25, 2008) Directed by: William Waring

Sheppard and McKay must escort a prospective queen as part of their diplomatic duties, unaware that an ambush has been set by some familiar enemies.

4.15 – Outcast

(February 1, 2008) Directed by: Andy Mikita

After returning to Earth for his father’s funeral, John Sheppard discovers the existence of a human form Replicator loose on the population.

4.17 – Midway

(February 15, 2008) Directed by: Andy Mikita

All members of the Atlantis expedition are being interviewed by the IOA and while most have had no difficulty, Col. Carter is worried about how Ronon, who is prone to losing his temper, will deal with it all. She asks her old friend Teal’c to coach his fellow warrior but they seem more interested in fighting each other. They use the gate to travel to the midway station where they must stay in quarantine for 24 hours before continuing on to Earth. The Wraith however have located the Inter-Galactic Bridge and find their own way to gain access to the station and attack Star Gate Command. With most of the personnel unconscious and the Wraith on Earth, it seems that Ronon and Teal’c are the only ones standing in between the Wraith and a full-scale invasion.

4.18 – The Kindred: Part 1

(February 22, 2008) Directed by: Peter F. Woeste

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.

4.19 – The Kindred: Part 2

(February 29, 2008) Directed by: Martin Wood

Slowly, everyone on Atlantis comes to terms with the sudden re-appearance of Dr. Carson Beckett who, he claims, has been Michael’s prisoner for some two years. He tells them what he was doing in Michael’s laboratory and they set off to find the kidnapped Teyla. Dr. Keller figures out just how he’s come to there at all. Sheppard meanwhile has been using all of his contacts to try and locate Teyla but they come across someone from the past. Teyla in turn has found some of the Athosians alive but they are few in number as a result of Michael’s experiments. Michael explains to her just what it is he wants from her as well as his own plans for the future.

4.20- The Last Man

(March 7, 2008) Directed by: Martin Wood

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.