On Moya, Chiana, D'argo, Jools and Crichton are arguing over what direction Moya to take and Crichton looses the argument. Moya heads through a cluster where an energy being enters the ships and enters Crichtons body. Crichton collapses and begins to bleed on the floor. When Crichton awakes, the blood has disappeared and no evidence can be found. The other crew members do not believe a word of what Crichton has said. Crichton begins to wonder if what had happened is because he is the clone and is beginning to degrade.
Crichton calls everyone to his room and they sit down and talk. D'argo orders the two women to sit and hear out what Crichton has to say. When Chiana finally gets up to leave, she discovers that there is a water on the floor when there hadn't been minutes before. Crichton orders one of the DRDs to replace what just happened and the video shows the crew collapsing and an alien energy form interacting with them. The crew visit Pilot who has been infected by an energy alien. The alien through Pilot tells the crew that he wants the fugitive who is hiding in one of the humanoid bodies. The crew members don't know which one contains the alien.
On Scorpius's battle carrier, the results of a test flight through a worm hole doesn't go to plan. The Peacekeeper inside the spacecraft that made the exploration has been liquidised. Scorpius wants to hold off but the chief scientist disagrees and eventually Scorpius orders him to be the next test subject for the journey.
One of the ways that the crew can discover who has the alien life form inside them is to question them about personal information, information that the alien life form will not know. D'argo and Crichton question each other and then question Joolushko and Chiana and they all seem to get the questions right.
Crichton questions asks Moya for help through a DRD where the DRD answers in binary, flashes for yes and no. After a conversation, he heads to the starburst chamber where he confronts Chiana who has one of the energy creatures inside of her. Chiana is about to launch starburst but Crichton is able to stop her. The alien leaves Chiana body and is seen floating above. Chiana and Crichton leave the chamber in time for the starburst to happen and kill the creature.
Crichton confronts the creature inside Pilot to tell him to leave now. The energy creature inside Pilot refuses, saying he likes the new host. Crichton and the others need to come up with a plan to remove the creature. The plan that they come up with is to short-circuit the creature and kill it. However when the plan is put into action, it is nearly jeopardised by Chiana falling asleep but eventually wakes up in the nick of time to finish her task. The alien is killed and Pilot returns to normal.
Scorpius has another dream of him and Crichton where Scorpius is pushed into a wormhole and jolting him awake.