As the Athosians and the Atlantis team get acquainted with one another and their new home, Dr. Carson Beckett tests a new gene therapy on Dr. Rodney McKay. If successful, this therapy will manipulate McKay's DNA and give him the Ancient gene needed for Ancient Technology Activation (ATA). This would mean that all personnel would be able to use the Ancient technology that pervades Atlantis. McKay already has a little device he's itching to use.
The experiment is a success and McKay adheres the green, jewel-like device to his chest, enveloping himself in a personal force field. Maj. John Sheppard tries to shoot him in the leg: no effect. McKay jumps off a balcony: not even a bruise. McKay is elated - until he realizes that he can't turn the thing off. And not only does it prevent anything from touching him, it also prevents him from getting any food or water through the shield - which means that, in time, he will die of hunger and dehydration.
Dr. Elizabeth Weir and Beckett are hoping that, as with most Ancient technology, the personal force field has a mental component built-in that would allow McKay to "think" it off. They believe he's just not doing it because, subconsciously, he may feel vulnerable in these new surroundings and by the threat of the Wraith.
That night, though frightened by stories that "ghosts of the ancestors" still live in Atlantis, two young Athosians, Jinto and Wex, sneak out of their quarters to play hide and seek inside a cargo hold. Later, Sheppard is awakened by Jinto's father, Halling: Jinto has vanished.
And strange things are happening all over Atlantis: The sensors that detect lifeforms are going haywire. Power and lights intermittently go on and off. The stargate starts to dial by itself (Weir orders it shut down immediately) and many Athosians say they're seeing a shadowy entity. The Wraith can project such images, but Teyla does not sense their presence.
During the search for Jinto, Sheppard encounters an inexplicable entity. It seems to be attracted to energy sources and feeds off of them. Over Atlantis' communication system, Jinto is heard yelling for help. He guides Weir and company to a panel in what looks like a closet, on the wall of which is a lighted map of Atlantis. McKay points out the spot where the most recent energy surge was detected. Sheppard touches it and a panel slides opens leading McKay and Sheppard into the same room in which Jinto and Wex were playing. The "closet" seems to be an inter-city transportation device. They find both Jinto and one of the Ancients' research labs.
Meanwhile, Grodin has found a way to keep the entity busy by shutting the Naquadah generators throughout the city on and off in order to lead it away. But the entity gets used to Grodin's tricks and catches Lt. Aiden Ford, who gets scorched badly.
In the research lab, McKay discovers a device that used to house the entity until Jinto accidentally let it out. McKay now believes the entity to be an early stage of the Ancients' experiments with ascension. The device is essentially a mousetrap that generates energy attracting the entity. When it goes inside, it's trapped. The catch is, someone has to be there to press the buttons. McKay is the obvious choice since his shield should protect him. But the suggestion scares him and his mind turns off the shield device, which drops off his chest. It won't work on Sheppard because the device imprints on its wearer.
Knowing how dangerous the entity is by what happened to Ford, Sheppard stands ready by the "mousetrap." Weir orders the power in Atlantis shut down so that the entity will be attracted to the trap. But as soon as it detects the trap, it pulls away.
Teyla suggests that, because the entity has been trapped in the vessel for so long, it wants to escape and that sending it through the stargate would be the answer. Weir is impressed by the young woman's ingenuity. A Naquadah generator is strapped to a MALP; the probe is sent toward the activated 'gate, which has been dialed to a barren planet, M4X-337. Alas, the entity engulfs the MALP and drains its battery before the device can go through the 'gate - and then the creature starts feeding on the stargate itself. McKay finds the courage to put on his shield device, go inside the shadowy entity, unstrap the Naquadah generator from the MALP and throw it through the 'gate. The entity follows. McKay - his shield drained by the entity - is unconscious but otherwise fine.