It's kind of a dumb question. It's like who would win between superman and a police officer. Samus is just in a different league. Master chief gets hit by a tank, he dies. Samus gets stepped on by a four story tall war machine (metroid prime 2, quadraxis) and she shruggs it off. he gets hit by a rocket, he dies. She gets hit by huge mounted energy cannons (various points in the prime series, manned by pirates) and she gets knocked back a few feet. He gets hit by an energy sword, he dies. Energy swords barely scratch her armor. Grenade, he dies, she yawns, jeep, he dies, she throws it out of the way, machine guns shorts bursts of sustained fire he dies, it bounces off her. She can survive antimatter blasts, and various other forms of super technology.

When it comes down to it, Master chief is engineered by an advanced human race wearing some high tech armor. Samus is engineered from a race so advanced it helped develop civilization across the universe before leaving behind their physical bodies and becoming one with the universe, and she's wearing their ultimate weapon. She's practically a demigod of war compared to his being a slightly buffed soldier. It's not even a contest unless you gimp her and give him everything he can possibly use.

The thing is Master chief isn't an idiot, he'd snipe her from long distance before samus even knew she was up for a fight. Thats what the military does.

However if it was a face to face battle samus would easily win, for obvious reasons.

Master Chief wins because he has higher-res textures.

For the love of, what is a sniper rifle going to do to her? She survives antimatter cannons! She's frikkin superman. The bullet will bounce right off her godly super high tech helmet.

And why does he snipe her while she stupidly stands there? She's a seasoned bounty hunter, she has X-ray vision, heat vision, spectral vision, she can run at super sonic speeds. How is he going to hide and snipe her?

WTF? one miserable rocketlauncher..wich has cooldown time of 2 hours compared to Samus..

she would explode that damn rocket with her missles...and shoot a power missle back at him..and he'd die..if she doesn't dodge..she would only lose about 20 energy..

what do you not get?!?!? it's freaking unfair..STOP comparing MC to Samus..it's pathetic..

have you ever seen a cat catch a mouse?...anyone choosing Samus is the cat..and anyone choosing MC is the mouse.

pro-Samus is toying with pro-MC..as MC fans think they got a chance when the cat releases it's grip...and then grabs the MCmouse again...

it's pathetic..there is NO way..whatsoever that MC will EVER beat Samus in a battle..ever..

The fans would win.

Master Chief because he is a male.......LOL

Samus

This.