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.

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.

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.

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

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

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

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

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.

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

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.

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.

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.

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.

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

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 fathera '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.

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

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

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.

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

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.