Setting

Space Quest II takes place within a universe that notably parodies prominent science-fiction brands such as Star Wars and Star Trek. The story takes place several months after the events of Space Quest I, with players assuming the role of Roger Wilco, a simple janitor who saved his homeworld of Xenon from disaster by destorying a potent weapon known as the Star Generator and killing the Sariens that stole it. A comic is included in the manual to explain to the player what events have occurred since Space Quest I

Story

Several months after saving his homeworld of Xenon from the dangers of the Sariens, Roger Wilco accepts a position as Head Janitor aboard Xenon Orbital Station 4 as his fame fades into obscurity. Contacted by his superiors to clean up a mess on a recently arrived shuttle, Roger finds himself ambushed in the station's hangar bay, where he is knocked out and abducted by unknown assailants. When he regains consciousness, he finds himself a prisoner on an asteroid base orbiting the jungle planet of Labion, run by Sludge Vohaul - a former scientist of Xenon. Vohaul reveals he was the creator of the Star Generator, but was exiled by Xenon when he sought to have the technology used as a weapon rather than for peace.

Eager for revenge, he attempted to use the Sariens to steal the generator, but was infuriated when Roger thwarted this. Despite the setback, he reveals he is in the process of creating an army of cloned insurance salesmen to help him eradicate life on Xenon. To punish Roger for his actions, Vohaul has him sent to his mines on Labion as a slave. However, whilst being transported over the jungles, a malfunction on the transport craft causes it to crash, killing Roger's guards. Escaping detection by Vohaul's goons, Roger makes his way through the jungle to the landing pad he arrived at, and steals a shuttle. However, Vohaul hijacks its controls, bring him back to the asteroid base to keep him from escaping.

With little choice, Roger sneaks around the base, attempting to find some way out. Instead of finding an escape route, he finds himself entering Vohaul's control room, where the scientist decides to keep him imprisoned more permanently. Shrunk down in size, and trapped in a glass jar, Roger manages to break out, and infiltrates a life-support machine that has helped to keep Vohaul alive over the years. Disconnecting it, Roger kills Vohaul, before getting himself restored to his normal size. Activating a self-destruct sequence, Roger makes his way through the base, finds an escape pod, and flees as the base is destroyed. Finding the pod cannot keep him alive forever, Roger enters cryo sleep to conserve oxygen while awaiting someone to rescue him, as the capsule drifts across space.