Earth force battle cruiser, The pillar of Autumn, comes out of hyperspace jump near a curious "object", running from bunch of Covenant's ships after an intense battle where they barely survived. The Covenent ships follow them there.
Tattered from the proveious battle, PoA is easily boarded by the Covenent troops. Captain Keys of the PoA orders shipboard AI, Cortana, off the ship via Master Chief, the last "Spartan II" elite force cyborg left to the fleet (Shipboard AIs like Cortana cannot be allowed to be capture or destroyed, since they are extremely valuable, and contain crucial information such as location of Earth, which is still a mystery to the Covenent, who are for an unknown reason, hellbent on wiping out humanity from the universe). Cortana AI core is plugged into MC's helmet, and MC battles his way to the last escape pod. Meanwhile, Captain Keys manually attampts to crash land the PoA onto the surface of the mysterious gigantic Halo shaped object orbiting near a planet.
MC's escape pod also crash land on Halo. Covenenat forces follow the escape pods and PoA down to the surfca of Halo as well. MC mounts a rescue of fellow Earth force soldiers and eventually of Captain Keys, who gets captured by the Covenent. during the rescue, MC and Cortana observe various curious espects of the Halo, which is obviously artifical, but within it contain many different natural seasonal surroundings. They also find out that the Covenent are also very interested in this "Halo".
After rescueing the Captain, MC and Cortana mounts an operation into finding out why Halo exists. They intercept Cov communications about a "Silent Cartographer", which is thought to be some sort of map room for Halo, and try to find it. After battling several Covenent forces trying to find the same, they eventually find it, and find out more about Halo, one of which is the "control room" below the surface of Halo. They get a ride on the Pelican drop ship into the bowels of Halo.
More battles with Cov who's ahead of MC and Cortana into the race to the control room of Halo, they arrive at the control room and Cortana interfaces directly into the main panel, getting plugged in it. After a brief maveling of the vast data within the control room, she suddenly is alarmed of impending mistake that Cap Keys is about to make at another part of Halo through the interface. She tells MC to leave immediately to Cap Keys location to stop whatever he is about to do. MC leaves hastly to the loaction via the Pelican, leaving Cortana behind in the control room.
MC is dropped off at a jungle part of Halo, where Cap Keys last comm was sent from. MC briefly battle Cov forces, then goes down into a vast structure that Cap Keys and his forces dissappeared into. Deep within, he find Cap Keys troops and the Cov forces decimated by a new enemy who are parasitic organisms that take over any organic matter into their own, turning them into zombie warriors called the "flood". Apparently this "flood" is the only thing that the Covenent fears.
After finding out about the flood, MC battles out of the structure, and hooks up with surviving earth troopers. As they leave they get surrounded by vast number of the flood, battles, but then is recued by a group of mechaical sentries and it's lead, a floating probe like AI entity calling itself the Guilty Spark. GS recruits MC into helping him to stop the flood. MC agrees and is transported instantly to another part of Halo.
GS warps MC to a facility call the Library to obtain whats basically the key that controls Halo. GS is by "protocol" not allowed to retrive this key byhimslef and that's why MC is needed. Unfortunately, the library is filled with the flood, and MC has to battle several levels to get to the key. After finally retriving it, GS warps MC back to the control room to turn Halo on, which he expalin will stop the flood, the reason for Halo's existance.
At the control room, MC plugs the key into the main panel. nothing happens. GS is puzzled, as Cortana's hologram zaps into view, knocking GS to the floor with invisible force. MC reacts and tells Cortana that GS is a friend and they are trying to stop the flood by starting up the Halo. Cortana obsorved the key into herslef, then chastises MC for blindly trusting the Guilty Spark, and explain how Halo stops the flood: by ridding the galaxy of flood's food source, which is any organic matter big enough to sustain the flood. GS demands that Cortana give back the key. Cortna tells him to go screw himself. Then GS summons his mechaical sentries and attacks MC. MC grabs Cortana from the panel and runs.
Cortana and MC determines that only options left to them is to somehow destroy the Halo, and to do it, they need the captain and his implant chip which will allow them to blow up Pillar of Autumn's reactors. But before they go to rescue Keys again, they decide to zap 3 power reactors within Halo which will slow down GS from starting up the Halo in another ways. They fight through waves of Cov and flood to do so. after which Cortana finds the loaction of Keys within a crashed Cov battlecruiser.
Cortana warps MC into the battlecruiser using the same method GS used. Battle has erupted within the ship, which the flood is trying to repair and to get off the Halo with, and the Cov is trying to prevent them. After battling more waves of both, MC find Keys, who's already been transformed into Flood. MC retrievs the omplant chip from the decayed head of the Captain and barely escaped the Cov ship via a Cov Banshee aircraft. MC and Cortana heads for the wreck of the Pillars of Autumn.
GS is already at PoA, and stops the self destruct sequence that Cortana initiates to make PoA's reactors go KABOOM. GS is also able to tap into COrtana and learns all about human history and of Earth. MC and Cortana then embarks on the only option left to them: to manually blow up PoA's reactors with granades and rockets. This envolves even more battles with the flood that already taken over the ship, and the sentries that GS has brought. Eventually, MC suceeds and then barely espcapes the PoA and Halo via the last lonstar fighter in it's bays. As the fighter zooms into deep space, PoA's reactors go kablooey, tearing Halo into chunks from the antimatter explosion.
Credits roll. Then you see a cut scene of the Guilty Spark following MC and COrtana into the deep space, obviously having excaped Halo's demise.
