Space Quest V: The Next Mutation

The game starts with a dramatic opening and Roger mid-mission on his ship: he is then revealed to be playing in a flight simulator, shaped suspiciously like the Millennium Falcon, at the StarCon Academy. Roger cheats to pass an aptitude test, and he's then given his own command— the garbage scow SCS Eureka, which looks (and functions) like an oversized vacuum cleaner. (Eureka is also a brand of vacuum cleaners.) The game involves several small missions, similar to ones seen in typical Star Trek episodes. Some missions are:

Roger is hunted, alone, on a jungle planet by W-D40, a homicidal gynoid (the apparent sister of Arnoid the Annihilator, an Arnold Schwarzenegger look-alike from Space Quest III). The gynoid has an invisibility device and a laser very similar to the plasma caster of the Predator. Her ship also resembles a Klingon Bird of Prey. Roger is being pursued for failing to pay for his Labion Terror Beast mating whistle from Space Quest II (a continuity error also found in Space Quest III, as in the second game it is shown on the order form that the whistle is free).
While visiting a "space bar", Roger must free his chief engineer Cliffy (a parody of Scotty from the original Star Trek) from the brig, where he ended up after starting a fight triggered when he overheard a rival ship's crewmember refer to the Eureka as a garbage scow. This parodies the bar fight scene in the famous Trek episode "The Trouble With Tribbles"—except that in this case, as Roger points out, the Eureka actually is a garbage scow! This is parodied further when Roger, noticing a warning not to immerse his free pack of space monkeys which he got from a "salesbeast" in alcohol, places them in his drink, causing them to multiply indefinitely (although the "space monkeys" are significantly larger than the sea monkeys they are a parody of).
At one point Roger is in the process of being teleported when a fly buzzes into the beam. The teleporter malfunctions, and Roger ends up in a tiny fly body with a human head. He then must find a way to restore his body, while the fly, in Roger's body with a fly head, acts rather stupidly (even by Roger Wilco standards) and jumps into garbage piles. This is a parody of science fiction/horror movie The Fly.

Roger's son from the future saved him at the beginning of SQIV, and later he shows a hologram of Roger's son's mother. Roger meets this woman in SQV and must protect her, or else his son would not exist, and thus neither would Roger.

The main plot is to stop a mutagenic disease that is spreading through the galaxy by discovering its source, and fighting everyone that got infected. In the end, the disease infects the crew members of the SCS Goliath, the StarCon flagship, whose toupee-wearing commander, Raems T. Quirk (a rather blatant spoof of Captain James T. Kirk), subsequently attacks the Eureka. In the end, Roger sacrifices his ship to get rid of the plague - and suddenly, if temporarily, becomes the commander of the fleet's flagship.

Roger is presented in a more positive light than usual. He's still a bungler and flies a ship that's falling apart at the seams, but along the adventure he gains the genuine respect of his crew and gets the girl in the end.