The plot begins some time after the Dahl Corporation's abandonment of the planet Pandora. Four Vault Hunters (Brick, Lilith, Mordecai, and Roland) arrive in search of the fabled Vault. After discovering the town of Fyrestone, the Vault Hunters begin to receive psychic instructions from a mysterious woman known as the "Guardian Angel". The Vault Hunters meet a CL4P-TP or "Claptrap" robot and a doctor named Zed who help them establish a reputation by killing several bandit leaders, eventually leading to the collection of an alien artifact, being the first piece of a key needed to open the Vault. This causes Patricia Tannis, Dahl's former archaeologist still in residence on the planet, to contact the Vault Hunters, revealing that the Vault can only be accessed once every 200 years and that the time of the next opening is approaching. Tannis also explains that three more artifacts are needed to complete the Vault Key. Meanwhile, Commandant Steele of the Crimson Lance (a well-outfitted military force led by the Atlas Corporation) threatens to declare martial law and demands the Vault Key pieces.
The Vault Hunters secure the second and third pieces by following Tannis' instructions, but the final piece, supposedly in the possession of a bandit lord named Baron Flynt, turns out not to be where it was expected. Steele contacts the Vault Hunters to reveal that there are in fact only three pieces and that Tannis has betrayed and misled them. Steele then disables the planet's ECHO network, preventing further communication with the Guardian Angel and anyone else. The Vault Hunters infiltrate the Crimson Lance's headquarters and find Tannis imprisoned. She claims she was forced into betrayal and urges the Vault Hunters to restart the ECHO network and stop Steele and the Crimson Lance before they reach the Vault. After restoring the network, the Guardian Angel directs the Vault Hunters toward Steele's location. During the final approach to the Vault, the Vault Hunters encounter Crimson Lance forces already locked in combat with the Vault's alien Guardians.
The Vault Hunters finally arrive at the Vault only moments too late to stop Steele from using the Key. When the Vault opens, a giant monster emerges and wipes out Steele and the rest of her troops. The Guardian Angel explains that the monster is called the "Destroyer" and was imprisoned in the Vault long ago by the Eridians, the alien race who left behind the ruins and created the Vault, in order to prevent the destruction of the universe, and that the Guardians were posted to prevent anyone from opening it. Although the Vault Hunters kill the Destroyer, the Vault is re-sealed for another 200 years. The Guardian Angel is revealed to be transmitting her signals through a Hyperion satellite in orbit high above Pandora. The story ends with the satellite sending a signal to a Claptrap robot on the planet, changing it into an "Interplanetary Ninja Assassin".
