Heres my reckoning of the plot, though Ill probably leave out most:
MC, Miranda and Johnson are all receiving awards aboard Cairo (the spacesation with MAc guns) orbittong Earth when a few covenant ships appaer from slipspace. Prophet of Regret has 'jumped the gun' and shouldn't be there yet, and the covenant didn't expect to find any humans here, which is why so few of them came.
The covenant then run away with In Autumn Clad hitching a ride in their slipstream burst.
A disgraced elite is given the chance to die with honour by becoming the covenant Arbiter. Arbiter are called upon in times of peril of the covenant (the prophet uses the Taming of the Hunters and the Grunt Rebellion as examples). Arbiter is told to go and kill some Heretics who have taken refuge in a forerunner facility near a gas giant.
Arbiter kills the heretic leader, who has only become a heretic because of what 343 told him (that the halos are weapons etc). Tartarus comes and steals 343, and they fly away.
In Autumn Clad 'land' out of slipstream near a new Halo, Delta Halo, which is being explored by the covenant. MC goes onto Halo to kill the Prophet of Regret (the one who prematurely came to Earth), and whilst there learns that the Hierarchs would probably have him killed anyway.
MC does so just as the covenant high and holy city, High Charity (a spacebound city), comes out of slipstream near Halo with an enormous covenant fleet. MC falls into the 'sea' and Gravemind captures him.
Whilst this is happening, Johnson and Miranda are trying to get into Halo's library so they can get the index before the covenant (naturally, the covenant want to activate Halo to get into heaven, because they dont know its a superweapon). Arbiter is told by the prophets that he must lower the shield covering the library and get the idex (sacred icon) so the covenant can get to the devine beyond. He does so, and Tartarus comes and steals the index, Miranda (who got their first) and pushes Arbiter down a big chasm.
Gravemind captures Arbiter.
Gravemind then shows MC and Arbiter Penitent Tangent, Delta Halo's monito who tells the two that Halo is a superweapon etc etc. This causes Arbiter to work with the humans, to try and stop the covenant activating the Halo.
All the while, flood have been released and are rampaging across Halo.
Gravemind teleports MC (or he makes Penitent Tangent to the teleporting) onto the massive holy city (High Charity) thats now near Halo. MC has to try and stop the prophets getting the index to Halo. He doesn't do so.. yet.
Arbiter is teleported to s spot on halo where he goes on a Brute killing rampage to avenge all the Elites that the Brutes have killed (yes, I've missed out the Brute/Elite war story arc).
MC then has to get onto the forerunner ship. This ship is the 'centre-piece' of High Charity, which is powering down the ship (this is what High Charity uses to slipspace travel, and basically all it's power) and preparing to 'set-sail'. MC is told the covenant are going back to Earth, to "finish what they started", and MC hops aboard the forerunner ship - just before it goes into slipstream towards earth.
Arbiter has to stop tartarus from activating halo with Johnson's help, and does so, killing Tartarus. 343 then tells Miranda, Arbiter and Johnsons that all six remaining Halos are ready for remote detonation. he says that you can detonate them all from a place called 'The Ark'. The forerunner ship enters Earth's solar system.
The End.
People think that Earth (or a place on Earth) is The Ark.
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