This is how The Overlord timeline goes in My Little Pony Transformers Prime: The Cutie Re-Mark.
[Twilight, Optimus, Spike, and Starlight arrive in a mixed-up Equestria]
Twilight Sparkle: Huh?
Optimus Prime: What?
Spike: Equestria's all mixed up.
Starlight Glimmer: And I think I know who's behind it. [points to something in the distance] Look!
[Twilight, Spike and Optimus see that she is pointing at a black dragon with purple eyes in the distance, indicating that it is the Overlord in dragon form]
The Overlord: [laughing evilly]
Twilight Sparkle: The Overlord.
Optimus Prime: Not possible.
Spike: He's in Tartarus.
Starlight Glimmer: But it seems my brother made it seem like he isn't.
[The Overlord turns and sees them]
The Overlord: Well, well, what do we have here?
[The Overlord approaches them]
The Overlord: Well, if it isn't Princess Twilight Sparkle, Optimus Prime, Spike, and Starlight Glimmer.
Twilight Sparkle: We mean you no harm.
Optimus Prime: We only came here via time travel.
Spike: A pony has the spell for it.
Starlight Glimmer: And we're trying to stop him.
The Overlord: I know who you're after: Nebula Star, Starlight Glimmer's brother.
Twilight Sparkle: How did you know?
Optimus Prime: Did he tell you?
Spike: Did he help you?
Starlight Glimmer: We came here a time travel spell.
The Overlord: I know because I've been shown how it works.
Starlight Glimmer: Well, do you know where my brother went?
Spike: Where did he go?
Optimus Prime: He probably used the spell.
Twilight Sparkle: Tell us where he went.
The Overlord: He went to another time.
Starlight Glimmer: Thanks.
Spike: Let's get going.