More traitor subplot eh? OK.
First, when we see the Kilrathi atacking the Pegasus, the CO of that station is a Pilgrim traitor that coperates with the Kilrathi. Now, when Blair and Angel are on the patrol later in the movie, and are hiding in the asteroids Merlin (Blairs holographic assistant) detects signals that were used by Pilgrims. When they get back to the 'Claw the Captain is pissed at Blair for letting the cats detect Blair and Angel, and dismises Blair's claims about the Pilgrim signals. Later when the Diligent goes to capture the Kilrathi ConCom ship and Blair goes inside because Merlin detected the signals again, he finds the bridge, kills the cats there, and finds the Navcom AI from the Pegasus. Then Gerals comes and acuses Blair of being a traitor. Then the CO from the Pegasus steps forword and is about to shot Blair and Gerald, but Blair shows him his Pilgrim cross. The traitor tells Blair that he has to prove himself, and tells him to kill Gerald. Blair uses his Pilgrim cross, while Gerald uses his knife. The fight, and Blair is about to kill Gerald, but he turns around and throws his cross at the traitor. He hits him, and the Traitor starts to die, but before that he pulls out a grenade.
Blair and Gerald barley escape from the explosion. However, before Gerald came and acused Blair, Merlin told Blair that the Pilgrim signals are being sent from the Claw using something that only the CO and the XO have acces to. So at first Blair thinks Gerald is the traitor, but then it turns out that he isn't, so there's only one more person that can be the traitor. Gerald and Blair rush back to the 'Claw and go to Captain Sansky's quarters, where he's recovering from the wounds he suffered in the previous battle. Sansky tells them he took a poison, and he'll die in a few minutes. He gives Blair the ring that belongs to Tolwyn and asks him to give it back to the Admiral, and then he dies.
That's basicly it. There are some less important things from the subplot in between that of course.