This sequel to both the Halo game and Halo: The Flood, details the events following the destruction of the ancient artifact called Halo.
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It begins on the planet Reach, which has been attacked and taken by the alien Covenant. Their usual method of conquest is "glassing" the entire world, but on Reach they don't quite finish the job: there is a section they need intact and captured.
It is here, in the "Castle", that several Spartan-II soldiers, enhanced genetically and equipped with high tech armour, have managed to survive. The Covenant are looking for something and they mean to find it first.
Meanwhile, in Halo's debris field, the Master Chief floats in his escape craft, believing himself to be not only the sole survivor of Halo but the last Spartan as well.
With no hyperdrive and no way to escape, all hope seems lost.
Then a Covenant fleet arrives carrying a dignitary who was supposed to inspect Halo. At the same time, other survivors are found by the advanced AI named Cortana, the Chief's longtime colleague. They turn out to be a Spartan, held in a cryo chamber, and a dropship full of Marines, hiding behind a piece of wreckage.
Using the added resources now available, the Chief and the others use the dropship as a decoy while they enter the alien flagship's cargo bays at high speed. Oddly, the huge ship has almost no warrior-caste on board, and with the help of Cortana's hacking abilities they capture the ship. While fighting off the rest of the fleet, Cortana discovers a new way of making Slipspace jumps, which could turn the tide of the war.
Escaping, they fly to Reach. There, they discover masses of alien troops on the ground, and the Chief is encouraged by the chance of seeing some of his fellow Spartans alive again.
Using the alien ship as cover, they fly to the surface and manage to penetrate the alien security, entering the Castle.
Here they find the Spartans, a fleet Admiral, and Dr. Halsey, who created the Spartan program.
They also find a mysterious crystal, which is the goal of the Covenant invasion. It seems to be able to affect gravity, radiation, and other forces yet unknown. They use its power to help them escape to orbit, and they take off with enemy ships in pursuit.
After much battling and with help from Covenant Engineers..who are not loyal to their masters..the captured flagship encounters a massive fleet headed for Earth.
It has to be stopped!