First, the plot, basically, Master Chief wakes up after 4 years of cryo in deep space and literally finds himself being pulled into humanities next severe threat. This is extremely dumb in of itself. What are the chances of that happening after drifting through space for only 4 years? And literally JUST IN THE NICK OF TIME. Anyway, moving on, he eventually uncovers that some radical covenant group wants to release an evil space wizard forerunner locked up in a space egg (oh shit its
Ivan Ooze) This guy wants to kill all of humanity because according to him they are a threat to the rest of life in the galaxy. He was assigned to this task or whatever and not he's basically a rogue agent of the forerunner. The covenant release him successfully.
BTW, he's a space wizard because he literally uses 'force grab/choke' on master chief on 2 occasions.
Later, Master Chief gains a Macguffen specifically to defeat the guy by a dead forerunner lady somehow. This is never brought up again or explained.
Through out all of this Cortana slowly goes mad from rampancy. Which is a mildly interesting side story initially. but gets old quick. It also brings about some REALLY cheesey lines from her. She becomes a waif. She needs her big tough man john to save her from rampancy. HAHAHA GOD DAMN IT 343. Don't get me wrong, this isn't as bad as what Team Ninja did to Metroid. (yeah I know about that, and I'm not even a metroid fan) but its pretty close. I will admit though, Halo 3 had you saving her as well but she was WAY less mopey and whiny about the whole thing. In fact she was almost serenely OK with her predicament in 3.
Master Chief then tries to stop the space wizard from leaving because apparently they are all doomed if he leaves the planet. Fails to stop him. Follows him into a slip space as a stowaway. They arrive near earth. The big bad space wizard shoots a death ray at earth and
slowly obliterates all life on Earth (no humanity, I expect you to die)
He finally encounters this bond villian, he's in a big bubble shield. MC inserts Cortana at a bunch of places to overload his shield with her rampancy clones or something. Eventually, you get a cutscene and kill him in a QTE and set off a nuke to destroy the death ray ship. Master Chief wakes up to see that Cortana has somehow protected him with a shield, and he's just floating in space. Don't know where her power source is. Anyway, she's also projecting herself as a 'hardlight' projection and touches Master chief in the chestplate and says she always wanted to do that or something to that effect. (HAHAHAHAHAHAHA WHAT THE FUCK) then tragically tells him she's not coming with him (again doesn't explain why). A couple more cutscenes chief is safe with the humans. Credits roll.
post credits scene: the entire west side of the US is obliterated. Every living organism in the area has been turned into ash but the structures and buildings are all still intact. Basically the death ray was a neutron bomb. Pretty fucked up. Interesting that the first place to get hit is where Bungie studios is today. (That is, LA and the rest of the west coast)