Jacob Thompson is the pilot of Sector Seven's top secret Ghost 1 spacecraft. He has a mild case of hero complex but also, fortunately, a sense of humor to go with it. He occasionally gets focused in his piloting to the exclusion of all else.
After years of preparation, the Ghost 1 launched in July 1969 with Thompson at the helm. All went well until they attempted the slingshot around Jupiter, at which point Thompson reported that the ship was heading out of the solar system at an angle. The ship was sucked through a wormhole and ended up in a distant star system. Thompson was the first of the crew to recover consciousness, and roused Captain Walker and the others when he saw the Ark waiting ahead. On his suggestion, Walker made the decision to set down on a nearby planet.
There they were contacted by Starscream and the Decepticon filled them in on how evil the Autobots were. Thompson was unhappy when the crew discussed their situation and realized they couldn't use the wormhole to return to Earth without risking leading the Autobots back there. Following a fight in which they aided Starscream in battle against Optimus Prime and Bumblebee, the Ghost 1 crew realized Starscream was lying to them. Thompson attempted to launch the Ghost 1, but the ground gave way, and it was only through a herculean effort that he avoided it being buried in rock.
The ship was found by Optimus, who soon cleared up the earlier confusion, and he helped them extract the ship from the cavern and back into space. Thompson still had hopes of getting home, but they were dashed when they contacted Mission Control, and realised there was a very real danger they wouldn't be able to go. He still kept a hope that, once they helped the Autobots defeat the Decepticons, they'd be able to use the wormhole. As it turned out, that wasn't the case — after Thompson used the ship's missiles on Starscream, right when the Decepticon was about to finish off Optimus, Starscream turned and destroyed the Ghost 1.