Okay, if there needs to be a third, then I demand the story goes something like this. (Following from things revealed in both the LS and DS endings)
We start off with The Dark Starkiller clone infiltrating the alliance and killing the Good Starkiller clone, then hunting down Vader through the Rebel encampment. In the meantime, through his espionage work posing as the "Good" Starkiller, he becomes morally conflicted as he begins falling in love with Juno, due to having to act as though he cares, and through that coming to actually start to care about her. Struggling to grip with emotions other than those tied to the Darkside, he seeks council from another. Rahm chastises him for being a typical, short-sighted fool, and tells him about Dagobah being a good place to sort out his thoughts. He goes, and finds Yoda, who believes him to be the first Starkiller clone.
Yoda councils him, explains to him that love is not born of the Dark Side, but can lead to it through fear of loss. At this point he realizes the truth, and that as long as Juno Lives, Vader will be able to control him. So he does what he has to do. He kills Juno, and flees back to Kamino, where it's revealed that the original Starkiller IS still alive, heavily restrained and incubated in a subterranean chamber, well beneath the original Kamino. He sets Starkiller free, and tells him what he's done, showing him some keepsake of Juno's that she'd never normally part with as proof of her death. (Ideally something to do with dead parents who were executed unjustly at the hands of the Empire)
That done, the two have an epic duel, in which you fight it out, Light Link vs Dark Link style, Only more Itachi/Sasuke in that the Dark Clone knows what has to be done, and has his own reasons for fighting Starkiller, namely giving the original back the powers he once possessed, along with a reason and drive to end Vader and the Emperor's reign forever. (of course, you'd play this fight from the real Starkiller's perspective, and the former Dark Sarkiller would be technically a lot stronger than you to start, although your force powers would upgrade to the ones you'd unlocked earlier as the fight goes on, until you're both equal, using a tiered health bar system like in the Vader fight in TFU:2)
Real Starkiller wins, and as Dark Starkiller dies, he tells the Real Starkiller the access codes to Vader's Flagship, the HIMS Devastator. Confused and vengeful, The real Starkiller takes Juno's keepsake, and hunts after Vader. Vader, now without Starkiller to keep him in check, has managed to break free of his prison, and return to the Empire, noted as a terrible loss for the Rebels (in which Rahm dies, to tie up that knot nice and neatly.) He searches for his Dark apprentice clone, but learns that the clone has disappeared. Vader begins to get a semblance of the plan that had originally occurred, getting as far as the Dark Starkiller had managed to infiltrate and had killed Juno.
He misinterprets this as a move to end his distraction and focus on the Dark Side, as he believes it to be, believing that Juno had no power over him, instead of the truth, and awaits his clone apprentice's return. The real Starkiller fights his way through Kimino, and all over the galaxy, as he's wanted by both sides, the Empire for escaping, and the Rebels for being a Turncoat (They can't be sure he's the real one, and someone killed Juno, after all).
Against all odds, Starkiller makes it back to the Devestator, within which the Emperor sits in Audience. Vader initially believes him to be the Dark Clone, however, once he comes in view, he draws his sabre, knowing that it is far from his clone.
And this time Vader is actually a challenging opponent.
The two battle back and forth, Vader obviously the superior in this fight. Starkiller comes to the realization that fighting with his rage is the exact thing that Vader wants him to do, and is part of why he is being controlled, then understands what he must do.
He will always hate Vader for the events that lead to Juno's death. As long as he lives, he will be bound to the Dark Side, no matter how hard he fights. There can be only one redemption.
Cue the cutscene full of flashback as He powers up his force repulse, to a critical mass that it's never reached before. He uses it as a new power, that the Emperor realizes that neither he nor Vader will be able to withstand, a power that will destroy the whole ship, and everyone within it. Just as he's about to unleash the power, he's shot from behind by Boba Fett, killing him instantly. He suffers the Emperor's fate a la RotJ, and falls down a reactor core shaft and is promptly obliterated.
Although dismissing the event and leaving the Emperor to his bidding, as Vader takes off his mask in his chambers, he respects the memory of Starkiller, who though he was twisted by the Darkside completely, almost utterly at first, still managed to find the light within, and would have ended the Sith's rule forever, had it not been for luck. Yoda feels the disturbance in the force and remarks that it is a sad day for the Jedi, and that only two now remain.
SOMETHING ALONG THOSE LINES.
You can fill in the first half of the game with The Evil clone doing things with the Alliance, "aiding" them on missions, while inadvertently trying to sneakily sabotage them at every turn.