For me, its obvious, Chief would own her.
Here are a few pics showing Master Chief vs Samus. More will come. For all you Samus fans, tough luck these pics were made by me and therefore Chief wins all!
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I my self am a big halo and halo 2 fan but first of all the ball is far larger then that, and if it was a real test samus would use plasma bombs and blow the chief up and for the second pic the energy shields in halo dont reflect dmg they just take it.
now if samus was to use a massive charge it could take the chief in 2 hits if even and same with the missils, but i really dont think theres much the chief can do to stop it samus is much faster and much deadlyer.