The surviving personnel from Idaho Prison Base flew to New Peenemunde Harbor following the prison's destruction. Unlike at Idaho Prison Base, the survivors were not integrated into the harbor's personnel, but were instead treated as visitors until their reassignment elsewhere.
When DS-2 was being integrated, Rudyard Shelton got in an argument with Ezekiel in an attempt to maintain his identity, and was knocked unconscious. This allowed Keegan O'Neil to retrieve the printout from him showing the location of Gustave Chiumbo's family.
After the meeting, Shelton was accosted by Achilles in a kitchenette, and Shelton killed him with a coffee pot and brewer. After he and Kerzach left to dispose of the body, Soundwave assaulted the harbor and gave all personnel an opportunity to leave peacefully. Most did, save Ezekiel, who fought Soundwave for his base and failed. Soundwave then constructed an army of robots to staff the base, where he continued work on the Hydra.
When James' team assaulted the harbor, Soundwave attempted to eliminate the intruders, but they proved to be too powerful. Just before Soundwave was killed by ROSS, Soundwave ordered Dragonstorm A-2 to destroy the harbor. The ship complied. (Disruptive Selection)