A group of Tavleks come aboard for trade negotiations. Rygel takes a vitally important crystal from Moya to make himself seem wealthy. The Tavleks kidnap Rygel and take him down to the planet, leaving one of their wounded on board. Everyone goes to the surface to get him except Zhaan who stays on board to keep an eye on the Tavlek left behind.

Crichton is put into a head-to-head battle with Crais by a magical being named Maldis who feeds off the emotions of others and makes himself stronger by absorbing all of the negative energy and anger from Crichton and Crais.

Crichton and Chiana try to infiltrate a peacekeeper base to get some vital medicine for Aeryn. Crichton gets caught by Scorpius and imprisoned. He is tortured using a device called the 'Aurora Chair' which is able to look inside his mind and where Scorpius learns that Crichton has the secret to creating wormholes.

Crichton, Aeryn and D'argo are stranded in an asteroid field while Scorpius searches for them. Their safety depends on Crais, who is nearby in Talyn. Aeryn teaches Crais how to control the young Leviathan - the only thing she can offer in return for the lives of her friends. When Moya returns to the asteroid field to look for her offspring, Crichton decides to remove Crais from control of Talyn. Scorpius finally sees his chance to strike.

The Scorpius clone puts John into a dream world to prevent the Scarrans from getting any wormhole knowledge.

D'Argo and Stark try to heal John, left with his head open on an operating table, while Scorpius attempts to avoid discovery. Zhaan makes a great personal sacrifice, while Jothee and Chiana commit an indiscretion.

Scorpius puts the neural chip into his own brain in an attempt to retrieve vital wormhole equations from Crichton.

Crichton goes to the command carrier to sabotage Scorpius' wormhole research.

D'Argo, Rygel, Crichton, Chiana and Sikozu get back to Moya only to find that Scorpius is there waiting for them along with Aeryn, now suffering from heat delirium. Aeryn has granted Scorpius asylum and claims that Scorpius saved her life.

Moya arrives at Earth in present day, Christmas. The crew show their ships and technology to Earth's scientists. Crichton starts writing a journal. The creature left on board Moya by Grayza manages to get to Earth where it starts killing and hunting down Crichton.