Halo 3
Halo 3 picks up shortly after the end of Halo 2. The short intervening period is documented by the Marvel Comics limited 4 issue series Halo: Uprising written by Brian Michael Bendis (illustrated by Alex Maleev) and the live action short film "Landfall" by director Neil Blomkamp.
As Halo 3 begins Spartan 117 has jumped from the Truth controlled Forerunner ship at a very high altitude and the impact into the jungles of Africa, in the ruins of New Mombasa has nearly killed him. Recovered by UNSC forces and Spartan 117's occasional companion Sergeant Major Johnson he rejoins the battle against the Covenant; this time joined by the Arbiter and the Elites of the Covenant as allies.
A final desperate attack on the Prophet of Truth fails and the Ark is activated. However it turns out that it was not the Ark that Truth was activating on Earth but a portal to the Ark well outside the galactic border. As Truth enters the portal the Flood arrive at Earth and invade the ruins of New Mombasa. The Flood has come to stop Truth from firing the Halo Array from the Ark. The Elite commander with the aid of SPartan 117 and the Arbiter destry the Flood infestation on Earth by "glassing" half of the African continent with an orbital bombardment. Unfortunately a message from the AI Cortana, hidden in the ruins of the ship the Flood arrived in reveals that a completely invested High Charity with an entire Army of Flood and a very powerful Gravemind are on the way to consume Earth.
The AI Cortana, in her message, recommends following The Prophet of Truth through the Portal to the Ark as a final solution to destroying the Flood and saving the galaxy. Initally the UNSC commander disagrees but eventually Spartan 117 convinces Fleet Admiral Lord Hood that Cortana's plan is humanity's best hope and he, Johnson, the Elites, the Arbiter and Captain Amanda Keyes now captaining the "Forward Unto Dawn" head through the portal after the Prophet of Truth. Shortly after they enter the portal the Flood infested High Charity arrives in Earth orbit but the Flood completely ignore Earth and immediately head through the portal to the Ark.
The Elites engage the rest of the Covenant ships while Spartan 117, Sergeant Johnson and the Arbiter hunt the Prophet of Truth. Once the Flood arrives the Gravemind convinces THe Arbiter and Spartan 117 that an alliance to stop Truth and the firing of the Halo Array is in both their interests and briefly the Flood joins the battle against Truth and the Covenant. During the battle Sergeant Johnson is captured and used to activate the halo Array (as it turns out only Humans, as the descendants of the Forerunners can activate the Array). In a last desperate attempt to stop Truth from using Johnson to fire the Array, Amanda Keyes crashes a Pelican transport craft into the activation room of the Ark and attempts to save Johnson. Cornered, Keyes briefly considers killing Johnson and then committing suicide when Truth shoots and kills her, seizes Johnson and activates the Array.
Spartan 117, the Arbiter and the Flood arrive moments later. As a human, Spartan 117 is able to deactivate the Array before it fires. The Arbiter kills The Prophet of Truth and of course the Flood immediately turns on everyone and attempts to kill Spartan 117 and the Arbiter.
As Spartan 117 deactivates the Array, Installation 4 Monitor 343 Guilty Spark reveals that a replacement for the huge ring world destroyed by Spartan 117 in the first game is under construction in the center of the huge space station the Ark. Agreeing that firing off the new Installation 4 at the Ark, beyond the galactic rim where it will not kill anyone inside the galaxy is the best way to defeat the Flood now that the Covenant has been stopped Spartan 117 seek to escape the Flood.
Spartan 117 and the Arbiter escape the Flood and head to a crashed, Flood infested Covenant ship where they belive the AI Cortana is being held by the Gravemind. Spartan 117 rescues Cortana and then join the Arbiter, Sergeant Johnson and 343 Guilty Spark on Installation 4. The Elites take their surviving forces as well as any remaining UNSC forces back through the portal to Earth and safety and leave behind Amanda Keyes ship Forward Unto Dawn for Spartan 177 and the Arbiter to return to Earth once the weapon has been activated. Battling their way through the Flood they arrive at the control room and make arrangements to fire the ring.
It is then revealed that the newly constructed Installation is too fragile to fire without destrying the new Installation and the Ark. 343 Guilty Spark demands that they wait a few days before firing the weapon so that his new Installation and the Ark are left intaact. When Sergeant Johnson disagrees 343 Guilty Spark goes mad and kills him. Spartan 117 destrys 343 Guilty Spark and activates Installation 4. The Installation begins to shake itself apart and Spartan 117 and the Arbiter make a mad dash for their only hope for escape, the Forward Unto Dawn.
Spartan 117 and the Arbiter make it to the Forward Unto Dawn. Spartan 117 implants the AI Cortana into the ships computer and as Installation 4 fires they enter the portal. The Arbiter heads for the ships bridge as Spartan 117 remains in the rear of the ship with Cortana. The ensuing explosion as Installation 4 destrys the Flood, itself and the Ark causes the portal to collapse as the Forward Unto Dawn is half way through it. The Arbiter crash lands on Earth in the front half of the ship with no knowledge of the fate of Spartan 117 and Cortana. A memorial is held for all those lost in the war that consumed billions of human lives and the Elites depart to secure their homewrld and deal with the betrayal of The Prophets.
After the credits it is revealed that Spartan 117 and Cortana have survived in the back half of Forward Unto Dawn. The ship is adrift somewhere remote in the galaxy. Cortana drops a distress beacon but informs Spartan 117 that it may be years before they are rescued. Since the ship still has power Spartan 117 enters cryogeninc sleep saying to Cortana in his last words in the game "wake me when you need me."