A large contingent of Atlantis personnel are aboard a Jumper beneath the water of Atlantis searching for a mobile geothermal energy drilling station on the ocean floor. The team includes Dr. McKay, Dr. Weir, Dr. Zelenka, Teyla, Ronon, and Colonel Sheppard. Zelenka and Ronon are complaining that the search is taking too long. After hours of searching, they finally find the station and begin docking procedures which in turn powers up the station. They are unaware that a Wraith is nearby… and it wakes up as they arrive.
Aboard the station McKay reports to Weir that the station systems are all online and functioning at full capacity. Weir cautions McKay to slow down before producing energy from the station, until they find out why the Ancients abandoned it. Ronon, Teyla and Sheppard are exploring the station when they realize they are going in circles. Teyla then realizes she senses a Wraith presence within the station. Sheppard orders everyone to retreat to the station's control room.
McKay, in spite of protesting, runs a life sign scan on the station and finds nothing out of the ordinary. Weir reminds the team that Wraiths can not be seen on life scans if they are hibernating. Despite the scans, Teyla offers to reach out with her mind to find the Wraith. Weir, Ronon, and Sheppard all watch Teyla reach out with her mind, in order to prevent her from causing trouble, similar to earlier episodes where Teyla was taken over by a Wraith. Teyla awakens from her trance dazed but says she was mistaken and there really is no Wraith there, and blames the water pressure. Weir and Sheppard split from Ronon and Teyla in order to explore the station more.
While searching, Teyla is being very quiet which concerns Ronon, and he confronts her. Teyla apologizes and places her hand on his shoulder explaining that he is a good friend, and that she would not want to do anything that made him uncomfortable. Suddenly Teyla viscously attacks Ronon, knocking him out and leaving him behind. She walks in a trance to an auxiliary control room and begins powering down sections of the station.
Weir and Sheppard are in one the blacked out sections, prompting them to call into McKay who still has power but finds out 40% of the station has been powered down. Sheppard tries to contact Teyla and Ronon but Ronon is still unconscious and Teyla is not responding. McKay reports the power outage was attributed to a control room in the search area that Teyla and Ronon were exploring. Sheppard and Weir go to find out what happened. McKay sends Dr. Dickinson and Dr. Graydon back to use the Jumper sensors in order to find Ronon and Teyla.
McKay, Sheppard and Weir all meet up and begin looking for Teyla and Ronon. Teyla opens a control panel exposing some of the control crystals. She then pulls her sidearm and proceeds to destroy the crystals. McKay, Sheppard and Weir hear the shots and run to follow them. In the lower levels of the station a Wraith comes into the station via an open water access door in the floor of the station.
Sheppard, Weir and McKay find Ronon and discover that Teyla attacked him. Teyla continues working at the control panel initiating emergency force fields around the station. Weir and McKay make their way back to the control room while Ronon and Sheppard go to find Teyla. Teyla awakens from her trance and stares at her empty gun, and then is discovered by Ronon and Sheppard. She has no memory of what occurred for the last hour.
McKay finds out that Teyla not only powered down sections of the station but she scrambled the operating system code and disabled the communications center. Weir meets Teyla, in the crew quarters with Sheppard and Ronon. Teyla apologizes and explains that when she opened her mind she found out the Wraith was a Queen. She found the Queen's mind to be very powerful but then remembers nothing else until Sheppard and Ronon found her. Ronon and Sheppard go to look for the Wraith and Teyla offers to help but Weir is wary of Teyla doing anything until she is certain the Queen is not still controlling her.
Dickinson and Graydon are working by themselves in order to disable the force fields. A force field cutting them off from the Jumper is disabled but both are unsure if it was due to what they were doing. Dickinson sends Graydon to check it out. Graydon finds wet footprints from the force field to the Jumper. Graydon is inspecting the Jumper when the Wraith Queen attacks Graydon.
Back in the control room McKay and Zelenka are debating why the Wraith would be on the station. McKay sends Dr. Coleman to reprogram the station's external sensors to see if there is anything of note in the area.
In the crew quarters Teyla and Weir are discussing the Wraith Queen. Teyla feels embarrassed for harming Ronon but Weir thanks her for using her power to discover the Wraith. Teyla tells Weir that the Queen was only able to control her because she had her mind open and was not ready for her. A mistake she will not make again.
Ronon and Sheppard are still searching for the Wraith when they hear Dickinson being attacked by the Wraith. Both run to help Dickinson but are cut off by the emergency force fields. McKay and Zelenka finally disable the force fields. Sheppard makes it to the Jumper and finds a desiccated Graydon after the Wraith consumed his life force. Sheppard whirls around to find the Wraith Queen who forcibly controls his mind so that he can fly her back to the Stargate so she can return to her people. Ronon jumps out from behind the Wraith and fires a shot, but Sheppard sees him and the Wraith knows what he sees and jumps out of the way. The shot destroys the Jumper's window that is exposed to the outside of the station, letting in sea water and knocking them all unconscious.
Sheppard and Ronon wake up to find themselves in the hallway due to the force of the water. McKay initiated the force fields to keep the water from flooding the station, effectively cutting everyone off from the Jumper. Ronon and Sheppard look around and discover the Wraith Queen is nearby and still unconscious. They decide to capture her rather than kill her since she may know a way out. However, the Queen refuses to tell them anything other than that they are about to die.
In a rare moment of humility, McKay is arguing with Zelenka that he should have trusted Teyla. Zelenka offers the repeated life scans that did not show anyone else on board. Coleman comes back and offers that the Wraith came on board after the scans. The external sensors have revealed a Wraith Cruiser almost buried in silt about a kilometer away. The crew surmises that Queen swam from the cruiser to the station.
After restraining the Queen, Teyla tries to enter the Queen's mind to find out how the Wraith came on board and if there is any more Wraith around, and why she keeps saying they are all about to die. The Queen says Teyla is too weak, but Teyla digs into the Queen's mind. She finds out that the Queen was the Queen of a great alliance and in the first wave of ships that attacked Atlantis. Her ship was damaged and crashed into the ocean. She fed off of her crew for centuries and was awakened from her hibernation when she sensed Teyla nearby. She left her ship and made it to the station so she could make it to freedom. She made it to the Jumper but did not possess the ancient gene to fly it, and needed Sheppard. Teyla then finds out that the Queen set the auto-destruct sequence on the Cruiser before she left it, and it will detonate in two hours.
McKay discovers that the planet's crust is very thin where they are located and there is a large energy potential there. The explosion of the Wraith Cruiser will be magnified by the large amount of magma nearby and will also wipe out Atlantis. Everyone is unsure about what to do. The self destruct needs to be deactivated but the Jumper is disabled and there is no other way to get to the ship, until McKay remembers seeing a type of deep water suit that was used to do maintenance on the station.
Sheppard and McKay walk to the Wraith Cruiser and get to the main control panel with 30 minutes to spare but find out that they need an access code to disable the self destruct sequence. The Queen refuses to reveal the code, prompting Teyla to try to entering the Queen's mind to acquire it. She loses her control momentarily and Weir stops her from trying again, fearing she is too weak.
Teyla tries to convince Weir that she can get the codes, but Weir is unconvinced and tells her no. Weir heads up to the control room and Teyla sends Ronon up to help her leaving her alone with the Queen. Teyla tries to enter her mind again but is quickly overcome by the Queen begins loosening the Queen's restraints. The newly freed Queen jumps at Teyla but discovers that Teyla is trying to hide something in her mind. The Queen digs into her mind and discovers the memory of a conversation between Teyla, Sheppard and Weir. They discuss the Wraith Cruiser and how it is still flyable but that they still cannot deactivate the destruction codes. The Queen knocks out Teyla and swims to the Cruiser.
The Queen surprises Sheppard and tells him that he is going to fly the ship, then deactivates the self destruct sequence. Suddenly McKay jumps out from behind her and opens up with his P90, but even unloading the entire magazine doesn't kill her. The Queen whirls around only for Sheppard to shoot her in the back. Teyla actually planted the memory of the meeting for the Queen to find so that she would escape and deactivate the self destruct sequence so she could escape in the Cruiser.
Everyone is in the crew quarters when McKay reports that everything is operational again and is excited to continue exploring the station. An eager Weir and McKay go off to continue research of the station while Sheppard, Ronon and Teyla all go to bed to recover.