On a search for Peacekeeper devices hidden in Moya, D'Argo rips out some sort of shield, causing an explosion that expels him from the ship. Since Luxans can survive exposure to space for a short time, Aeryn retrieves him with her prowler. D'Argo partially recovers, but he's confused about where and when he is and he thinks that Zhaan is his wife, Lo'Laan, and Rygel is his son, Jothee. He flips back and forth between the past and the present and is able to give some hints about where he was and what he was doing just before he was blown into space, but not enough to be helpful.
The DRDs are acting strangely, some of Moya's systems are malfunctioning, and .Pilot is feeling unwell. With him out of action, Aeryn finds that she has an instinctive knowledge of Pilot's console, probably because she has some of his DNA. But in spite of this, the life support continues to deteriorate.
Crichton pokes around Moya trying to find clues, but he's attacked and fired on by the DRDs and Aeryn must shut them down. She, John, and Zhaan have a conference. They come to the conclusion that Moya is trying to kill them so they decide to shut down her higher functions.
In one of his flips to the past, D'Argo sees Rygel and believes him to be his son, Jothee. When Rygel realizes this, he graciously submits to piggy-back rides and being tucked up in bed. D'Argo is very sweet with his "son", hugging and tickling him and explaining why their family is different from the others who live nearby. When D'Argo thinks that John is his brother-in-law, Macton, he attacks him. Crichton then provokes D'Argo into regaining his memory by pretending to be Macton and accusing him of being unworthy of Lo'Laan. This jogs D'Argo's memory and he tells the story of his past. His wife's family was Sebacean and his brother-in-law was a Peacekeeper who killed her to keep her from D'Argo. While her blood was still on his hands, he arrested D'Argo for her murder.
He remembers where he was when he ripped out the device and John goes to investigate. To everyone's surprise, Moya is pregnant and has been trying to protect her child, not injure her crew. John manages to communicate with her through the DRDs. He explains that the crew is happy about her pregnancy but her efforts to protect the baby are killing Pilot and them. Moya turns the life support on and they all settle in to wait for the baby to be born.
This is the first we've learned of D'Argo's life before his imprisonment. His son is probably still alive, but he doesn't know where he is or if he'll ever find him.