The Federation Police officer Captain Dare enters the Palace of Power with an arrest warrant for Lana, who is being charged with crimes committed by Mother Brain that were reattributed to her. She and Samus appear in court, and the judge turns out to be Ridley impersonating Judge Racklas. Samus attempts to attack him, but is restrained. Mother Brain calls to explain her plan.
Samus and Lana are taken to RX 338, also known as Prisonworld. Samus is sent to Metroid cell block one (containing enemies from Metroid) and Lana is sent to Mount Icarus cell block ten (containing enemies from Kid Icarus). Samus is angered at their separation, as it was her duty to protect Lana.
Samus arrives in her cell block, and the enemies she sent there attempt to attack her in revenge, but she beats them back using Kraid as a weapon. Meanwhile, Lana arrives in her cell block, where she encounters many enemies from Kid Icarus, being treated inhumanely. This causes her to retaliate against a guard who was beating on one of the prisoners. She meets Syren, who liked how she stood up to the guard. Lana speaks to the prisoners, asking them to help her organize a plan to make the prison a fit place to live, so that the guards will treat them more respectfully.
Meanwhile, Samus organizes an escape plan using Kraid as a diversion. She orders him to distract the guards, saying that he can either "spend a month in solitary or a month in the hospital". Samus crawls through one of the tunnels to steal a ship that will allow her to leave. She is forced to choose between going back for Lana or leaving her.
Samus decides to take her back, and forcibly throws her into the shuttle. The enemies from Kid Icarus yell in protest. Syren exclaims that Lana is very well respected in the prison, but that she does not belong here, asking Samus to take her home. Lana leaves with the promise that she will not forget Syren and will order that new rules be set for Prisonworld.