Master chief is a master in hand-to-hand combat and a tactical genius who genetically altered to be the strongest human alive, not to mention he was trained since he was six. Tony stark is a rich guy with lasers and super suit. Master chiefs suit also has an energy shield based on alien technology, whereas Tony Starks suit has no shields, just metal plating.
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I hope you're joking. Stark's suit does have a shield. It took a nuke at 2% power. Also, he has class 100 strength, meaning he can lift 100 tons or greater. Probably greater. He's already powerful enough to tear off John's suit like a tin can (and that's in his normal suit), but he's also been trained by Captain America, meaning he's probably just as skilled as John too. Also, any one of his weapons would punch right through John's puny shield like nothing. A repulsor round would send John flying; a uni-beam would instantly put a hole through him. John has literally no chance here.
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No, here's what happens in a fight. Master Chief runs off into a UNSC arms depot and hyperamps his jetpack with help from Cortana. Chief uses his infinite jetpack to fly to the Ark. Chief activates all the rings and kills Stark.
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One small problem........ Cortana's dead.
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Fine, Chief finds Doctor Halsey and has her hyperamp the jetpack.
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See? This guy gets it. Iron Man's tech is far more advanced than Master Chief's ever could be. Master Chief could definitely have taken on Thor and the Hulk and survived like Iron Man.
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Although Iron Man does have flight, that's a major advantage.