The season began with Fiona Phillips on tour with her famous rocker mother Molly, brother Jack, a skeptic, bus driver Ned, his wife Irene, and their son Clu. Stringing together all of Fi's paranormal encounters was her search to communicate with her father, who died when she was three years old. Fi first “encountered” her father in the second episode titled “Web Sight” where an unknown force sent her internet articles warning her of the future. From alien invasions, time warps, and ghosts, Fi faced 13 episodes worth of paranormal activity. Also encountered: one powerful tulpa, a Bigfoot, angels, and more significantly, the Will o' the Wisp. The season finale featured Jack becoming possessed by a hyperactive Scottish Will o' the Wisp, also known as a Spunkie. The Spunkie told Fi she could save her brother from his control by speaking his one true name, which was only seven letters. Fi found the spirit's one true name, Bricriu,therefore saving her brother. Bricriu had offered to protect Fi from evil spirits who had battled her father and had also offered to give her contact with her late father in return for being allowed to possess her brother. She thought he was lying therefore rejected his offer. He reappears in later episodes to keep her away from other spirits and people who claims are a threat to her, depending on how one reads it, this may be seen as evidence he was telling the truth, but this is questionable at best, especially since in one episode he tried to prevent her from talking to a person who knew her father and wanted to give her information.
The second season was even darker than the first, playing out over twenty-six episodes. The premiere picked up with Molly taking time off the tour to record an album. Fi and friend Candy meet a medium who is proven to be a fraud. However, the one who uncovers the fake is actually a medium himself who aids Fi in contacting her father through music on his old guitar.
The character of Clu was reduced during the season, as he went off to college, and his brother Carey was introduced to fill in the gap. Many classic beasts surfaced within the season, including vampires, werewolves, banshees, trolls, sirens, and merfolk. In a pivotal episode, Fi learned that her father investigated the same kinds of supernatural events that Fi did. In fact, this was exactly what led to his death. Upon learning this, Fi is angered by her mother's deceit in covering up the truth about her father. Molly was eventually possessed by Bricriu, the same Will o' the Wisp as Jack was in season one. Fi discovered that Will o' the Wisps or other dark powers, though not necessarily Bricriu himself, may have killed her father, resulting in the accident that police had assumed took his life. In this episode Bricriu tried to kill a former firefighter who had been present at Rick's car crash and was aware that Fi's dad had been dead, with no apparent cause, before the car crashed. Following this episode, Fi had further contact with her father, as the answer to a troll's question - Faith - was revealed on her computer and a plethora of cell phones. Fi briefly time traveled to her third year, when her father was still alive, in episode 13, Fountain.
The season ended with Fi discovering her father's twin sister received encoded messages from him in her sleep. The messages led Fi to a rooftop where she was attacked by a three-headed demon and saved by the ghost of her father. He left her with a message that the spirit world was angry with her and would try to stop her investigation about the paranormal. At last, Fi got the proper farewell to her father that she had been searching for. Many DeLizia fans consider this a proper, if not entirely fulfilling, finale.
After skewing somewhat dark and intricate in its second season, the show was forced into a lighter tone for its final batch of episodes. Cara DeLizia left after the first episode, which introduced family friend Annie Thelen. Fi had yet another encounter with Bricriu. In this episode her family turn into plants and animals and Fi has to go to Bricriu for help in saving them. He does and then he convinces her to give up investigating the occult to save her family, which spirit world threatened because of its anger at Fi's intrusions. Fi, who still didn't trust Bricriu even though he claimed he was trying to help, trapped him in a floppy disk. The attraction to the occult, manifested in the ring her father gave her, was passed on to Annie as Fi went to live with her aunt. Molly moved the family to a new, brightly colored house.
Annie's story arc was the mystery behind a spirit guide that followed her in the form of a panther. Her character was also musically talented, and episodes featured more of her singing than that of the older Mackenzie Phillips. The season's stories were a far cry from previous episodes, playing such plots as being sucked into a painting (which directly followed an episode of people being sucked into photographs), a stone from the Tower of Babel that caused xenoglossy and a detention class that never ended. Cara DeLizia never reappeared in the season, however Fi was still prevalent in many episodes via e-mail. She made a brief appearance in the episode “Earth 101” by a lookalike, and in the final episode, although in the final it was only a rerun clip from the first episode of the season. The mystery of the panther was solved: when Annie was three and living in the Amazon she saved a young tribesman at risk to her own life. His tribe, in turn, saved her and his father took on the form of the panther to always protect her as thanks for her selfless act.