John Crichton is an International Aeronautics and Space Administration astronaut who in the opening few minutes of the pilot episode is accidentally catapulted through a wormhole across the galaxy, thus setting the scene for the show as a whole.
During a test flight to prove his theory that you can use the Earth gravity to propel a ship an previously unrecorded speeds, a wormhole appears and John and his module (named Farscape One) are pulled through it. On his exit from the wormhole, he finds himself in the middle of a spaceship dogfight and accidentally causes the death of Tauvo Crais, the brother of Peacekeeper Captain Bialar Crais. Crichton's craft is then pulled aboard a large spaceship, Moya, where John meets his first aliens (Zhaan, D'Argo and Rygel). The aliens knock him out and put him in the brig along with a captured Peacekeeper Prowler Pilot named Aeryn Sun. When John and Aeryn revive in the cell, Aeryn proceeds to attack and beat John for being out of uniform. Aeryn assumes that John is a Sebacean and Peacekeeper like she is. Humans and Sebaceans look exactly alike. John shortly after meets Bialar Crais, who considers revenge for his brother's death. John has to adapt rather quickly to a life with aliens, guns, and space travel, without the comfort of Earth culture. Towards the end of Season One, Crichton encounters a mysterious alien race known only as The Ancients, who gift him with a hidden wormhole knowledge, and a Sebacean-Scarran hybrid Peacekeeper by the name of Scorpius who tries to get into possession of it.
Early in Season Two, Crichton learns that Scorpius implanted a neural chip into his head, which causes hallucinations of "Harvey", a neural clone of Scorpius. These hallucinations influence Crichton in an effort to get at the hidden wormhole knowledge. As a result, Crichton's behavior grows more erratic and unpredictable, also caused by his feelings for Aeryn Sun. With the beginning of Season three, the neural chip has successfully been removed, but a neural clone still remains in Crichton's head. A few episodes later, Crichton is "twinned" by another alien. Neither of the Crichtons can be called a copy and neither is the original. Eventually, the crew of Moya is split across the two Leviathans, Moya and Talyn, and are separated from each other. Each ship has one Crichton. One Crichton begins a romantic relationship with Aeryn, but he is killed. When the survivors of the two crews are reunited, Aeryn in her grief is very cold to the remaining Crichton. The crew of Moya starts going their separate ways at the end of Season 3. Just after Aeryn Sun leaves Crichton for good, he learns of her pregnancy.
Early Season Four leaves Crichton with nothing but time for working on his wormhole theories. He eventually reunites with the crewmembers of Moya and also Aeryn and Scorpius, who has fallen out of favour with Peacekeeper high command. Halfway through the season, Crichton finds his way back to Earth, but he voluntarily gives up the dream of Earth and returns to Moya. After a series of dangerous events, Crichton and Aeryn find time alone together. Aeryn tells him he is the father of her child, and Crichton proposes to her. In this moment of her accepting, an alien craft apparently kills the two and ends the season. Crichton and Aeryn are revived at the beginning of The Peacekeeper Wars mini-series, and Crichton uses his wormhole knowledge to successfully force a peace treaty