Why did Master Chief activate the Halo ring? Isn't that what he's spent the past two games trying to avoid, for crissakes?
Imagine Luke Skywalker succumbing to the Dark Side. Or Homer Simpson putting in an honest day's work. Or Batman cracking a smile. These classic characters would never engage in activities so opposite their intrinsic nature, so why oh why would Master Chief voluntarily choose to fire a dreaded, life-erasing Halo?
Our best guess: Remember when you first arrived on the Ark and one of your Marine pals said, "Check it out, in the sky, is that...?" He was referring to the distinctive swirl of stars above you. See, that's supposed to be the Milky Way, meaning the Ark is located very, very far away from humanity's home planet.
Being a clever guy, and a bit of a risk-taker, Master Chief decides this distance is enough to keep Earth safe. So when Gravemind and the Flood are infesting the Ark, he fires the newly constructed Halo in an effort to destroy it all. Gravemind, the Flood outbreak, the Ark and the ring itself are obliterated with a single action.