My latest draft, directly from Notepad:
It all starts in the future. In Space Quest 12. Somehow, the pedestial where Vohaul's holographic projection was shown, has been shattered (possibly by the Xenon Rebellion), and now apemen from the past have been sent to clean up. While cleaning up, one of the ape-janitors finds a floppy disk, which is a back-up of Vohaul's mind. Quickly, he travels back to one of Vohaul's old HQ's on the ice planet Radon, where he delivers the disk to a superior apeman. The Radon personnel, that are still stationed there, have already begun making a cyborg replica of Vohaul. Now they just need a brain for it. And on a dark night, the evil Vohaul is brought back to life as a robot.
Meanwhile, Roger and his wife Bea, are on a shore leave on the planet Romanticon 7. They're currently dining in a restaurant called Pie-ery, where every single meal is made of pie. Bea then reveals that she is pregnant (Roger Wilco Jr.)... How'd that happen, Roger? Suddenly, they are attacked by a horde of Vohaul's evil apemen. Vohaul have somehow found out that Roger and Bea are at Romanticon. Anyway, as always the apemen fail. Roger and Bea fights them and wins, and due to an apeman that's far too talkative, they find out about the cyborg and the base on Radon. They rush for the planet in the Aluminium Mallard, but they don't know that Vohaul is prepared.
As they approach the icy atmosphere of Radon, they ship is shot down by Vohaul's defense system. Both manage to survive, and Roger goes off to explore the planet while Bea stays with the ship. But while he is gone, Bea is ambushed by a small army of apemen and their superior. Vohaul's new sidekick, James T. Quirk! He survived the Eureka explosion, because he was just shattered into a million pieces when the ship exploded. Moved by the solar winds, all the slime-pieces finally gathered, and he was dragged to Radon due to the gravitational force. Vohaul found him and gave him his human shape back. He was hurt in the explosion, though, so he has been "healed" with some various cyborg implants.
Quirk and the apemen marches off with Bea, leaving Roger alone on Radon. He explores it, and finally finds his way to Vohaul's base. These scenes have been completely fleshed out. They are in the VSBinfo.txt file. Unfortunately, Roger gets caught in Vohaul's base, is confronted with his evil archenemy and ends in prison. But as always, he escapes. This time with the aid of Fester Blatz, who is selling weapons to the apemen, because it's damn good for business. Roger finds out that Quirk and Vohaul have taken Bea to Radon, the moon of Radon. In the core of Radon is a radioactive liquid called "Detanon". With bombs made of Detanon, Vohaul will be able to destroy entire planets! Naturally, he's going there to drill for the Detanon. So what started as a personal vendetta, is now a clear threat towards the whole universe.
Roger manages to sneak himself aboard a space shuttle and flies to Vohaul's Radon base with it. After getting smuggled in, Roger finds the security system of the Radon outpost. Of course, he can't stop playing around with it (he inserts a virus disk in it), so he manages to destroy the system, leaving the base without alarms, power and such. Unfortunately, Vohaul and Quirk have also been developing cyborgian elite-Apeman, which are to be used against the possible survivors of Vohaul's Detanon-attacks! Boy, you're in it now, Rog!
Anyway, Roger manages to get to Vohaul's lab. I have no idea how he should get there. A maze, perphaps? He manages to pass through the security and manages to put the virus disk into Vohaul, knocking him over. Vohaul has a bunch of apes in his lab that are used to test how apes react on Detanon, as his henchmen are basically genetically modified apes. One of them teleports Roger into Vohaul's mind. His subconciusness. A place with all kinds of weird stuff. When Roger picks up a certain item, he will be transported to a memory of Vohaul. He has to walk thought 3 memories from Vohaul's past. As in that Christmas tale by Dickens or whoever it was, the people in the memories cannot see Roger. While in these memories, Roger will have to solve puzzles to get past some obstacles. These puzzles will affect Vohaul later, reprogramming him to Wilco and Bea's personal nanny. How quaint
After his adventure into Vohaul's subconciusness, Wilco and Bea are ambushed by General Quirk (once again...). They fight with him (in an SQ4-like fight scene, I guess), and end up pushing him into a large pool of Detanon. This would be where it would be supposed to end. The villains have lost, and the good guys have won again. But in the middle of the victory, Quirk rises from the Detanon pool. Not as his human form, but as a heavily mutated Quirkblob with shape-shifting abilities! Now, Wilco will have to outsmart his old arch-nemesis. Yet, I don't know how. After that is done, they finally leave Radon. In the end cutscene, Bea gives birth to Roger Wilco Jr. and orders poor Vohaul to make tea and throw out the dirty diapers. What a suitable ending, I think...
Just a little side note. The sequence with Vohaul getting thrown into space
could work. Let's say that he hits an Electromagnetic Storm like Quirk did. The storm time-travels to SQ11 or something, where the disk is found by a Deep Space Salvage team. I think this would be the right way to do it, as we never hear of how the disk got there in SQ2 or 3. It would sort out most paradoxes.