This is Halo 4's story, meaning the game on it's own. Not 5 books a movie and a line of action figures that keep the milk flowing from the cow.
So Master Chief is floating in space that's cool, but somehow his armor changes while he's in in cryo sleep(here's where we first encounter the entity called "space magic"). Then because while Master Chief was away on vacation the humans went shit in hands retarded and un-did everything they learned from the first 3 games by pissing off teh aliens(apparently in the Halo universe humans are the equivalent of a toddler that keeps hitting a cat and then doesn't know why the cat scratches back). So now the same alien guys we just got done fighting in the first 3 games are back(Prime example of 343's creative new approach to making Halo their own). The only in game explanation we get of why they're back is "Gee Chief maybe they're like a DIFFERENT covenant or something lol idk" from our trusty sidekick Jarvis, I mean Cortana.
Master Chief brings back his plot armor with surviving a fall from space with no shields(what suspense much wow) then his mission becomes clear save his blue friend/lover/AI sonic the hedgehog from going to fast. He fights some more space aliens until he finds a glowing orange ball, normally anyone else in this situation would not -blam!- with it but because Forerunners were shitheads they locked a really bad dude in a prison that he can somehow still -blam!- shit up in.(It's becoming more and more clear why Forerunners are extinct, they're the dodo birds of space).
This is where our second damsel in distress comes into play Lasky, who re-enacts the titanic in space by crashing the biggest ship humans have into a planet. Meanwhile Master Chief frees the villain(I bet he really hates Mondays). They spend a few missions trying to stop the glowing orange ball sith lord from leaving the planet(they -blam!- this up too). On the other hand the Samus AI is going batshit insane. The only sane character(I forget his name but he looks like Burt from Sesame Street)Tells Master Chief he needs to stop worrying about his waifu but Master Chief is like -blam!- you sir I love her, and even though he was friendzoned by chief Lasky let's their love be.
Master Chief finds a space librarian who instead of telling him to be quiet and giving him books gives Master Chief, stopthebadguyandplotarmor.exe. Master Chief thanks her by letting the bad guy get the super weapon which he then uses to orange glow skeleton disintegrate people to death(good thing Chief downloaded his plot armor to be immune to this!)
Basically all the happens from here on out is the speed run on the death star with an X wing(Master Chief assumes the identity of Luke Skywalker) Cortana turns into Hal 9000, you beat the bad guy by pressing the left trigger Cortana space magics Chief away from a nuke and the sane captain guy got fired cause -blam!- you for trying to be rational.
The bad guy isn't really dead and Master Chief lost his qt3.14 gf and he has really pretty eyes.
Did I miss anything?
Sorry for grammar/spelling it's late and I'm wee bit retarded(not as retarded as the forerunner's tho;) )
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Boomp