Moya docks at a Scarran Border Station where all craft that wish to enter Scarran Space must dock for quarantine first. Scorpius takes on the role of Moya's captain for the deception to work. John becomes a Peacekeeper, something up until now he probably thought he'd never be. The other crew have different names. Sikuzo befriends a Kalish Administrator of the station in order to get the information that they need. The Scarran ship containing Aeryn is about to leave so they fake an illness in Rygel which when it fails to fool the people onboard the station, Nooranti reacts the dormant Hyrnerian dermaphollica virus in Rygel. The station is closed down preventing anything from leaving the craft. John persuades the sebacean nurse looking after Aeryn that he wants to make out with her and manages to find out where Aeryn is being held. However, he is captured and has to rely on Scorpius getting him out and back onto the ship. Hynerians are not the only aliens susceptable to the virus but also sebaceans. The Scarran leader wants the feotus that Aeryn is captured kept alive no matter what so he orders that Chiana is kidnapped. Nooranti is brought before Aeryn during the transplant process and manages to delay the transfer. Sikozu Svala Shanti Sugaysi Shanu manages to deactivate the ships security whilst John rescues Aeryn. On his way out, he's confronted by a Scarran who is killed by the stations security when the power comes back on. As they leave, the Scarran commander of the craft containing Scorpius attacks him. As John settles Aeryn Sun down to sleep, he gets a vision from Scorpius telling John Crichton that if he's not released then the Scarrans might know everything he does including wormholes.
The Moya crew make it to Katrazi, the secret Scarran base, determined to resuce Aeryn Sun. Already there is Grayza who is trying to make a pact with the Scarrans. As neither of the parties, Scarran and Sebeacan can be trusted, John gate-crashes the meeting wearing a nuclear bomb threatening anyone who tampers with it and it'll go off. Also on the base are Kalish and Charrids, both of whom dislike one another which is to the Moya's crews advantage. Sikuzo, D'argo and Rygel start to play them off against one another. Scorpius, the reason they came to the base is being held in a cage and tortured using Scarran brain waves. During the interrogation, Stark makes an appearance and tortures Scorpius. John Crichton ratches up the stakes by insisting that Scorpius be handed over to him which they agree. Dominar Rygel XI, Captain Ka Dargo and Sikozu Svala Shanti Sugaysi Shanu suceed in starting a war between the Charrids and Kalish then leave. As they make their escape, Scorpius turns against them revealing himself to be a Scarran spy.
After having their escape plan sabotaged by Scorpius, the Moya crew who have rescued Aeryn Sun have to find another way out. Scorpius just wants the wormhole technology for the destruction of the Scarran Empire which understandably, John doesn't want to give because of the loss of life it would cause. Scorpius explains that the Scarran base is the only source of Crystherium Utilia in this area of space. The plant helps Scarran brain and by destroying it, they can set the Scarran Empire back cycles in development. Instead of siding with Scorpius, he plans to side with Grayza to get out of there. When the Scarrans manage to disarm the nuclear bomb that John Crichton had with him, he decides to go along with Scorpius' plan and destroy the crop. Once down amongst the crops, they become trapped, the only way up is through a lift which now has Scarran soldiers coming down in. Sikozu Svala Shanti Sugaysi Shanu reveals her true identity as being a Genetically modified Kalish who can emit Scarran harmful radiation which she does. Grayza's plan to destroy the Scarrans would cause an unbelievable amount of destruction to Captain Meeklo Braca relieves Commandant Mele-On Grayza of her command. The crew enter the lift and make for the exit above. Utu-Noranti Pralatong and Dominar Rygel XVI hunt down the real Stark who had been duplicated and whose clones work for the Scarrans. Once above and nowhere to go, John Crichton again goes along with Scorpius's plan and drops the bomb down into where the plant is grown. The explosion destroys the whole crop along with a lot of Scarran life. The crew then make their way out back to Moya.