In Season Two, onetime outsider Ozzie Graham finds himself part of this eclectic group of misfits—all the while struggling with the knowledge that life exists beyond our world. Meanwhile, Special Agent Alex Foster, a smart, dedicated FBI investigator has come to Beacon on the hunt for local newspaper owner Jonathan Walsh for white collar crime, but soon learns he harbors even greater secrets.
After learning the members of StarCrossed were on the ship as kids, Ozzie tries to get the group together. FBI agent Foster is sent to Beacon to investigate Jonathan Walsh. A merger takes place on the ship & the aliens are under new management.
Agent Foster continues her investigation into Walsh by meeting with StarCrossed. Yvonne leads a small team to search for Gerry -- unaware he's been abducted. Meanwhile, on the ship, Jeff asks Gerry for advice on how to deal with his new boss.
Gerry returns to Earth but Yvonne has a rule about not dating other experiencers; Gerry returns to StarCrossed; Father Doug and Chelsea go on their first real date; Ozzie and Agent Foster make contact with Jonathan Walsh.
Gina uses her birthday party to distract Agent Foster so that Ozzie can sneak out to meet Walsh; The Cube pressures Jeff to clean up the ship; Don wants to tell Kelly a secret; Father Doug and Chelsea face difficulty.
Ozzie confronts Walsh about being an alien. Richard gets fired from his job and joins Agent Foster on her search for Walsh.
The group copes with a tragedy. Agent Foster reports back to the FBI. Jonathan Walsh and Don have reservations about the alien mission.
The group asks Agent Foster for help with an investigation. Chelsea and her husband go to marriage counseling. Jeff blames Don for bringing an intruder onto the ship.
The group attends an alien experiencer convention. Gina meets one of her therapy heroes. Gerry & Yvonne have their first fight. Richard tries to prove to Agent Foster that aliens do exist. Both Chelsea and Agent Foster receive unexpected news.
Agent Foster goes to Gina with a personal problem. Richard sues his employer for wrongful termination with the help of the group as character witnesses. Jeff is blackmailed by Eric and Jonathan Walsh offers his support.