Go on youtube... there is this guy who posted all of the story elements of all the Halo games...
Basically it boils down to this:
-You play as Master Chief John 117, a part human part machine super soldier known as a Spartan...
-In Halo CE the UNSC Ship Pillar of Autumn is fleeing from a covenant fleet and discovers the first "Halo"... and once they are overrun... the crew tries to abandon ship onto the Halo while Captain Keyes (the commander of the Autumn) tries to land his ship on the Halo, before this though, he gives the ship's AI (Cortana) to MC to keep the Covenant from getting it...
-While exploring the Halo and rescuing survivors, they discover that the covenant believes the Halo is a weapon... and that they must stop them from using it... They set off to find the control of the Halo before the Covenant...
-They arrive at the control room only to discover that Captain Keyes is about to make a mistake and release the Flood that was trapped on the Halo, MC has to hurry to try and stop him, but is to late and Keys and all of his men are killed...
-This is when MC meets the Monitor of the Halo... who makes MC help him contain the flood... by retrieving the index of the Halo to activate the Halo, which the Monitor tells MC is a weapon made for killing the Flood... MC helps him retrieve the index and they return to the control room... Cortana then reveals to MC that the Monitor wasn't telling him everything... that the way the Halo combats the flood, is by killing all sentient life that the flood needs to feed off of...
-Cortana then comes up with a plan to destroy the Halo by causing the Autumn (which crashed earlier) to overload it's core, causing a massive explosion...
-They accomplish this and take off in a small craft that was located in the Hangar of the Autumn... the game then ends...
-In Halo 2.. you take on the role of 2 characters, MC (who has been rescued from that small craft and returned to Earth)... and the Arbiter... an elite soldier of the Covenant... in the beginning MC is being awarded for his service, and the arbiter is being tortured in preparation for his exicution for his failure at the Halo (he was apparently the commander of covenant forces at the Halo)... he is spared though and made the "Arbiter"... which the high prophets assume will kill him anyways because all Arbiters die because they are sent on the most dangerous, pretty much suicide missions...
-Shortly after this, Earth is attacked by a Covenant fleet commanded by the Prophet of Truth, and are being beaten back because their fleet wasn't very powerful (Cortana assumes that they didn't know humanity was there and that they came for another reason, not to destroy humans)... the covenant command ship, which has one of the prophets on it attempts to flee, and Captain Keys (the daughter of Commander Keyes) follows (with MC and Cortana on board)... after their hyper speed or whatever speed jump, they arrive at another Halo and the Covenant holy city High Charity which was waiting there...
-Once on the Halo, MC kills the Prophet of Truth, but is injured and thrown into the water below the platform of the fight, and taken by a mysterious creature...
-Arbiter is sent to get the index of this new Halo, and discovers that Captain Keyes (and a trooper named Johnson who has been in all Halo's) already have it... he takes it from them, but Brutes show up and take the index and inform the Arbiter that he was sent to die and that the Elites have been expelled from the Covenant... he then pushes the Arbiter off the ledge they are standing on into a deep hole, where he is also taken by the mysterious creature...
-The creature turns out to be the Gravemind of the Flood and tells MC and Arbiter that they must work together to stop the Covenant from activating the Halos for both the flood's sake and the sake of all living beings... MC is sent to the holy city and Arbiter is sent back to the Halo... MC has to stop the other prophets and Arbiter has to stop the Brutes from activating the Halo... MC fights his way through the city and Cortana tells him to put her on the City's computer system so she can find the prophets... she does, and tells MC to leave her there so she can delay the launch of their ship long enough for MC to stow away on it... as long as he promises to come back for her...
-You then switch back over to Arbiter who is fighting the Brutes, and finds humans (under the command of Johnson) also fighting the Brutes... they decide to put aside their differences and work together to prevent the Halo from firing... they stop it, but find that they have put all the Halo rings in a standby mode that will allow all to be fired at once from a remote location...
-The game then switches back to MC who is on the covenant ship arriving at Earth (for an unknown reason at this time)... MC tells the platform they are passing not to fire on the ship because he is on board and that he is going to "Finish this fight..."... the game then ends...
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This is where Halo 3 begins...
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