In a way, the whole tv series Fringe is a Girls Underground story, but in particular I think the end of season 2 through most of season 3 particularly qualifies. Olivia Dunham is an FBI agent (orphaned, by the way) who gets sucked into working on strange, unexplained cases, assisted by an old mad scientist, Walter, and his reluctant (at first) son, Peter. Over time, she comes to find out that the scientist experimented on her as a child, and that she has special powers because of this. They also discover there is a parallel universe that has become connected to ours, where things are mostly the same, but slightly different, and most of the people in our world have doppelgangers there.
When Peter journeys to the other side on a potentially dangerous mission, Olivia follows him using her unique abilities, hoping to rescue him. While Peter and Walter make it back safely, Olivia is attacked by her double, who then assumes her persona and goes back with the others. Olivia is then stranded in the “otherworld,” kept prisoner by Walter’s harsher double (called “Walternate”), who is her adversary. She escapes and enlists a cabbie for assistance, who eventually goes from hostage to willing helper and companion. But while in captivity, Walternate had been feeding Olivia her double’s memories, and she soon begins to forget herself, thinking she is the Olivia from that world. Being a parallel universe, the “objects from home” theme is everywhere.
Eventually Olivia recalls her true identity, and begins to struggle to get home, constantly thwarted by Walternate. She is also temporarily betrayed by a companion, though he comes around to helping her. In the end, she does not directly confront her adversary in a final showdown, but is able to escape his clutches and return home.