Bioshock: Into the Depths is a fan fiction on the game, taking place 40 years after Subject Delta's revival in Rapture and quick conflict with the acclaimed Rapture Family led by Doctor Sofia Lamb. The story tells of a Spec Ops soldier and his drive to survive the city's many dangers as well as uncover the fate of his team and his missing wife along with his family's past.
The story begins with the reports of a research vessel going missing somewhere in the Atlantic while investigating a series of unknown radio transmissions sent out from that same area. In repsonse, the US government sent out a team of skilled Spec Ops soliders to locate the missing scientists as well as to continue their investigation. Among the team of elite soliders is Sergeant 1st Class Train Feld, who has a personal matter in the mission as his wife was among the disappeared research team. However, as the squad nears the last-known location of the scientists, their boat is suddenly attacked by a large unknown assailant that leapt onboard from the water. During the quick fray that occured, Train is knocked out by the attacker and is sent overboard into the cold ocean. When he eventually awakes, Train finds himself in an entrance port of Rapture with the fate of his squad unknown. However, he is quick to make contact via radio communcation with an elderly gentleman who calls himself "Virgil" and states that he wishes to help the Spec Ops complete his mission as well as find his teammates and a mean to escape. Without any disagreement, Train heads toward Chronos Central to begin his search...
- Train Feld - Main protagonist; member of a Spec Ops team sent out to the Altantic to find a missing research team (among them his wife Lora). After being knocked unconscious by an unknown attacker, he finds himself inside the city of Rapture with no sight of his teammates. With only Virgil as his sole ally and guide, he must discover the whereabouts of his team and wife as well as escape alive.
- Virgil - Train's sole guide to Rapture; a mysterious elderly man who communicates to Train through radio and blue-lighted security cameras (hacked by him as he claims). He claims to be help Train find the rest of the squad and wife, though his true motives are not known as well as his past.
- Lucifier - The shady antagonist; the newest ruler of Rapture who taunts and threatens Train through speakers . He claims to be a god and commands his subjects with an iron fist. Some of his lines oddly remind Train of fellow soldier and friend Stephen Jericho, who died one year ago.
- Malcolm Stone - Fellow Spec Ops and friend to Train; was aboard when the ship was under attacked. His fate is currently unknown to this moment.
- Lora Feld - Train's wife; one of the missing researchers of the mystery transmissions. Her whereabouts are unknown, but Train is seeking to find her in the city.
The enemies are the same from the previous games, although there are several new types exclusively for the story. The list of enemies appear in the following lists:
- Chain (New): Wield dual pistols chained to their wrists and bear broken cuffs around ankles and neck.
- Big Daddies
- Alpha Series
- Torcher (New): Wields a large flamethrower and can activate Walker Bots attached to its armor.
- Mini Turret
- Security Bot
- Security Camera
- Walker Bot (New): Land-based version of Security Bot; appearance is similiar to a crab.