When Scorpius captured Crichton in the episode Nerve, he tortures Crichton in the Aurora Chair. We later learn (for the first time in Won't Get Fooled Again) that Scorpius implanted a neural clone of himself into Crichton's brain. A sophisticated chip was placed in Crichton's head, allowing "Harvey", Scorpius's neural clone, to work through Crichton's head and find the wormhole knowledge. With the chip attached, Harvey is useful on several occasions, keeping Crichton alive in preparation for capture. For example in Won't Get Fooled Again, Harvey tells Crichton that a Scarren is the one who has captured him, and also reveals its weaknesses.

However, he doesn't always help. At the end of Season 2, Harvey has gained a great deal of control over Crichton, and uses this power to cause a lot of damage, including Aeryn Sun's death. He also calls for Scorpius to arrive, allowing Scorpius to get his hands on the wormhole knowledge and the chip from Crichton's head. After the chip's removal though, Harvey still remains in a sort of "wraith form", meaning that the personality still exists, but the power behind it is gone. John has Harvey in his head, but he has control. This goes on for many episodes in Season 3 and Harvey continues to help when he realises that he wants Crichton to survive. Without Crichton, there is no Harvey.

In the episode Eat Me, Crichton is "doubled", and thus, so is Harvey. The two versions then follow very different paths. One Harvey is blasted from Crichton's mind by an Ancient during Daedalus Demands, not that this matters, because the Crichton he had been in was then to perish in the following episode. The second Harvey however had a much more complex story to follow. Appearing in cartoon form in Revenging Angel, and most interestingly, being able to chat to D'Argo when linked via a Hangi in Scratch 'n' Sniff, Harvey's adventures are many, but they become more sinister in Season 4.

Scorpius's arrival in season 4 sees Harvey become less important at first, but there is more going on than Crichton realises. Scorpius kindly agrees to rid Crichton of the mental clone, thus removing Harvey, and this works, freeing the second Crichton from the complex conversations from within his own mind. However, when Scorpius is later captured and taken to the Scarren base Katratzi, Harvey reawakens. Harvey claims that this was a fail safe, and that Scorpius never removed Harvey, he simply implanted Harvey 2.0, a more sophisticated version capable of transmitting all of Crichton's thoughts directly to Scorpius. This is what prompts Crichton to attempt a rescue in the episode Hot To Katratzi.