Hey, for all we know, The helmet could have a special device to change her voice. And since (as far as I know...) he never had taken off her helmet or armor, Master Chief actually COULD BE FlutterShy in disguise!
Excuse me, I wanted to let you know that had uploaded this colored and I have an idea that they are stealing since 1. they never mention that you originally drew this 2. they removed your signature 3. they have done this with someones comic and had not given credit and had removed their signature Here is their upload: [link]
Master Chief: I am here to help you, everypony. Twilight Sparkle: Who are you? (Master Chief takes off helmet and reveals Fluttershy's face) Fluttershy: I am a friend because we are Friendship is Magic together as the Mane six.