The story opens with a stranger kidnapping Rhys and Fiona and forcing them to recount their shared involvement with the Gortys Project. Rhys, a Hyperion employee on Helios, is demoted by Hugo Vasquez after overhearing that Vasquez is buying a Vault Key from August.

Rhys and Vaughn take a stolen briefcase of money to Pandora to buy the key first, but they learn it is a fake created by Fiona, Sasha, and their mentor Felix. The money is stolen by Bossanova, and the group forms a reluctant alliance to recover it.

Rhys installs a Hyperion ID chip from Professor Nakayama into his cybernetics in hopes of locating the briefcase, then loses consciousness. The money is later found near a secret Atlas facility, but Felix takes it and triggers the briefcase’s explosive lock, either dying or escaping depending on Fiona’s choice.

The others discover the Gortys core inside a secret chamber in the Atlas base. A hologram of Handsome Jack appears to Rhys and tells him they have found the Gortys Project, which will lead them to a Vault.