This is how Crash and the gang's suspicions of Twilight goes in Thunderwing Returns.
Crash Bandicoot: Twilight's been acting funny lately.
Evil Ryan: How come?
Crash Bandicoot: Well, Evil Ryan. She.... I think. There's something off about her.
Evil Ryan: Like what?
Bertram T. Monkey: Her eyes glowing? Talking in someone else's voice? Gaia Everfree is Gale's friend?
Evil Ryan: So?
Bertram T. Monkey: So? While we are away, Twilight and Optimus fought Thunderwing and they don't invite us.
Evil Ryan: And that's a problem because....
Evil Anna: I don't know. I think it's, like, someone's controlling Twilight's mind.
Evil Anna: It's that what I found out?
Sonata Dusk: The same thing happened to Bumblebee once.
Princess Celestia: Also, some dark magic is infecting my former student.
Princess Cadance: And something's happening to my sister-in-law.
Clank: Yes. If Thunderwing returns, we could stop him with our Rainbow Power.
Princess Celestia: We have to find someone to stop him.
Princess Cadance: I agree.
Doctor Crash: The universe hangs in the balance by someone who is friends with Twilight.
[Cody pulls out a photo of Ryan]
Ryan F-Freeman: Thunderwing? Who's Thunderwing?
Princess Celestia: Thunderwing is a creation of Unicron himself. [shows image of Thunderwing]
Ryan F-Freeman: Whoa. I think I beaten Unicron himself. Maybe Tirek.
Thomas: It won't be easy. Thunderwing is virtually made of Dark Energon. He will do whatever it takes to complete his mission.
Evil Ryan: And what will that be?
Thomas: To destroy the Matrix of Leadership and the Element of Magic.
[Ryan and the gang gasps]
Ryan F-Freeman: But if he destroys the Element of Magic, the Elements of Harmony will forever be useless.
[Princess Celestia nods]
Princess Cadence: Ryan. You must keep Twilight's crown safe from Thunderwing.
Evil Ryan: And the Matrix too, Ryan.
[Ryan's chest opens]
Ryan F-Freeman: Prime. You can put the Matrix in me now.
[Optimus puts the Matrix in Ryan's chest]
Optimus Prime: Ryan. I'm only giving this to you to keep it safe. After Thunderwing is destroyed, I shall pass the Matrix of Leadership to Twilight Sparkle. As it was passed to me.
Ryan F-Freeman: But, Prime. Twilight is my friend and a princess. She's not worthy.
Optimus Prime: Nor was I, Ryan. But, one day, she will become a Prime when the Matrix is passed.
Ryan F-Freeman: Maybe, I shall rise from Twilight's rank and use the power of the Matrix... to light our darkest hour.
Evil Ryan: Whoa. Whoa. Whoa. Why you pick Twilight? Ryan could have the Matrix. After Thunderwing is exterminated. Ryan could be a Prime-prince. Even with his crown and the Matrix. Just my point.
Optimus Prime: Until that day, till all are one.