Geneforge/WMG

Monarch is the main character from the third game.
Well, he seems to have been a really powerful Shaper, and we know something horrible happened to the third game's main character. Besides, where else would he have come from?

The fifth game's main character is . ..
Speculation on the game's forums includes, but is not limited to, the third game's main character, Monarch, both, the fourth game's main character, Shaila, Pol, Bernard, Danette. . . Really, there's no end to it.

Khryk faked his own death in the third game.
Sure, we saw the Tele Frag that took his life, but did we confirm that all those bits and pieces scattered across the floor were of him, rather than some unfortunate creation? No, he escaped to safety, and that's how he survived to the fourth game, even though the Geneforge in the Ashen Isles was completed, a circumstance that requires his death. Alternately. ..

The canonical ending of the third game is the Game Over screen.
In a subversion of We Cannot Go on Without You, Alwan continued to fight the rebels after the main character's death. It's why neither he nor Greta will talk about their early experiences. Going one better. ..

The Shaper referenced by both Alwan and Greta is not the main character of the third game, but a previously unmentioned fellow who joined them after the early death of the main character.
There aren't many supporters of this theory, but it would explain a few things--for instance, how it was that. ..

Something went really, really wrong in the third game's conflict between Lankan and Diwaniya.
Let's face it--it's possible to kill Lankan and leave Davros alive, but how the hell could Lizbet have died (as Davros tells you in the fourth game?) She's not even living with Lankan's followers, but is in the same town as Shaper Diwaniya, who incidentally would go hostile if you killed her. No, she was slain by someone else, either Diwaniya or one of his followers. Admittedly, Diwaniya said that he wouldn't need to kill the rebels. However, if you had killed Lankan yourself, there would have been no need to harm Lizbet, and if you had helped Lankan, but his rebellion had ultimately failed, Alwan would have left the party, when canonically it was Greta who left.

The Rebels' Geneforge shapes some sort of Weirdness Censor ability into the user.
It's pretty much the only plausible explanation for how a Servile armed to the teeth and with a small army of creations behind him can walk through the streets of Dillame without so much as raising an eyebrow.

Serviles where the natives of Sucia island.
The only native that you meet in the first game uses a sevile graphic and the theory itself is raised in game that the serviles where created out of a humanoid species rather than being a product of pure shaping.