The player controls Rufus across various highly detailed backgrounds, collecting and combining smaller objects and interacting with machines in order to solve puzzles and advance the plot further.

As Cletus and Goal ascend back to Elysium (after the end of the first game), Rufus builds an elaborate machine to hurl himself at their ascent pod with a giant saw blade.

Cletus' pod smashes into the side of Bailiff Argus' Organon cruiser, which is overseeing the planned destruction of Deponia.

Seagull then brazenly admits that Rufus is not his real child, that he was a "trash baby" found abandoned in a junk pile near their home village of Kuvaq.

Discovering that the "Unorganized Crime" leader Donna has a brain implant as well, Rufus is able to use a remote to transplant "Lady Goal" into her; Donna/Goal then kills the two goons with her, and decides to leave to rejoin Cletus.

Venturing around Porto Fisco and the Rust Red Sea with Bozo's trawler, Rufus tracks Donna/Goal's submersible and attempts to disable it using torpedo dolphins.

Onboard Argus' cruiser, Rufus finds Cletus apparently fiddling with the bomb controls to set it off.

But Cletus gains the upper hand and leaves Rufus hanging for dear life as he gloats, only to be punched out by Goal.

As she is about to save him, however, Rufus admits that he activated the bomb countdown, which leads her (and the personalities still inside Donna) to turn on him, leaving with Cletus.

To Rufus' surprise, Goal arrives a moment later, admitting that while she was tempted to head home, she was missing an important part of herself as well.