This is how Twilight becomes infected goes in The Enemy Within The Sparkle.

[At Canterlot, Princess Celestia and Princess Luna are with Twilight as Thunder Streak and Starlight come in]

Thunder Streak: Any luck finding out what happened?

Starlight Glimmer: Or what those things are?

Princess Celestia: Not yet.

Princess Luna: But something seems to be the matter with Twilight.

Starlight Glimmer: What is it?

Princess Celestia: We're not sure.

Princess Luna: Looks she's been infected with some kind of virus.

[Stormer and Trixie come in]

Trixie Lulamoon: Twilight, thank Celestia you're alright.

Stormer: A virus? Let me see.

[Stormer checks Twilight]

Stormer: This is no virus. This is a series of tiny nano-bots which can turn anyone against their friends and hold that person against their will.

Twilight Sparkle: Put me inside a shield before whatever Meltdown did to me takes over. [coughs] Too late.

[Twilight looks away. She snickers sinisterly and she turns around and her eyes have turned green. Starlight and Thunder Streak and Trixie prepare magic beams]

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