Neat but some of the paragraphs are REALLY long. You should avoid having them be over 3 lines long and only make rare exceptions for them being past 5.

“But this time I don’t think I mind it,”

I think if he was trying to prove his dominance he would object to Twilight giving him orders. Taitin is trying to get Spike to his side right? Since his loyalty to Twilight is born out of submission it would make sense to make him dominant over her to cancel that out.

Interesting take. I was kind of expecting him to seduce the mane 6. After all a chain is only as strong as it's weakest link. Going for Twilight makes sense as well as she is a big part of keeping the mane 6 together.

So is what Twilight said right? Is Spike only a project?

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Hard to say. She wasn’t quite herself when she said it, although this is an alternate universe too so things can be different here.

He heard one bad thing and suddenly

screw Equestria and all the friends I made, I'll help a villain conquer it all.

Spike wouldn't turn evil so easily, more or less he'd run away to Rarity and think about what to do next.