Battle of Installation 00

The Battle of the Ark was a large engagement between the UNSC-Covenant Separatist Alliance, the Covenant Loyalists, and the Flood. It was the final battle of the Second Flood outbreak, the Human-Covenant War, and the Covenant Civil War.

Battle of Installation 04
During the Battle of Installation 04, Cortana intercepted the Installation's index as it was being inserted by Spartan-117. She continued to hold on to it after she had been removed from the Installation's Control room. She also had spent over 12 hrs inside the Control Room's computer, gaining an incredible amount of information about the Halo installations, making her possibly the most knowledgeable regarding the operation of the Halo rings, the Forerunners and the Ark - perhaps even more so than Guilty Spark 343 who admitted he was quite ignorant of the Forerunner structures beyond Installation 04.

Battle of Installation 05
The Battle of Installation 05 included many events that would become major factors in the Battle of Installation 00.

The UNSC AI, Cortana, remained aboard the Covenant Holy City, High Charity as the Flood and its central consciousness, the Gravemind, took control of it. From there, the Gravemind interrogated her, and she willingly answered its questions.

The aborted activation of Installation 05 had set all of the Halo rings to standby, where they could be activated from the central location of the Ark.

Finally, the Covenant Civil War and the Human-Separatist Alliance began in the space around Installation 05.

Second Battle of Earth
The Prophet of Truth had arrived on Earth and began digging for a Forerunner structure. Eventually they uncovered it and activated it, opening a portal that would take them to the Ark - a Forerunner structure from which Truth can fire all of the Halo installations at once. As he departed through the Portal, a Flood captured ship arrived on Earth and crashed. From it, they were able to extract a message from Cortana, alerting them that High Charity was heading for Earth and indicating that the solution to the problem of the Flood lay beyond the portal.

While Lord Hood was suspicious of Cortana's warning and objected to going through the portal, Commander Miranda Keyes, Spartan-117 and Ship Master Rtas 'Vadum all indicated their wish to proceed through the portal. Hood gave Keyes command of the UNSC Forward Unto Dawn for the Human commitment to the mission and the fleet of ships chased after the Prophet of Truth.

The Battle
The Prophet of Truth, having successfully activated the artifact in New Mombasa, left Earth through a Slipspace portal to the Ark, a Forerunner structure that can be used to fire all of the Halo installations at once. Despite Lord Hood's urging, Commander Keyes took the UNSC Forward Unto Dawn with a small fleet of Separatist cruisers lead by the carrier Shadow of Intent and proceeded through the Slipspace portal and arrived at the Ark. The Separatists immediately engaged the Brute fleet stationed to protect the Prophet while the Dawn deployed shock troopers to locate Truth. Despite being outnumbered 3-to-1 in space, the seperatist fleet made short work of the Loyalist space forces, likely due to the Elites' superior tactical skills. 343 Guilty Spark, now working with the UNSC-Separatist Alliance, led SPARTAN-117 and the Arbiter to the Ark's Cartographer where they pinpoint the Prophet's location. By then Truth had already holed himself in a secure facility in the core of the Ark and had activated a large barrier around the entire core to ward off the attacking forces.

The UNSC ground forces, along with Separatist reinforcements, assaulted three emitter pylons that powered a small section of the barrier. When the defending forces were eliminated and the pylons shut down, the Shadow of Intent began its attack on Truth. At the same time the former Covenant city ship High Charity arrived from Slipspace and crashed on the Ark. Debris spread from the city ship heavily damaged the Shadow of Intent and helped spread a new Flood infestation on the Ark as a means to stop Truth and to be safe from the Halo activation array. Without any heavy support, SPARTAN-117 and the Arbiter personally attacked the facility where Truth was to activate the Halo installations.

Sergeant Major Johnson, who had disappeared during the assault, was in fact captured by Truth's forces and was being tortured into pressing the final switch to activate the other Halos. With SPARTAN-117 and the Arbiter too far away to stop Truth, Commander Keyes grabbed a Pelican dropship and crashed into the facility to rescue Johnson, but was killed soon after by Truth himself. The Gravemind dispatched Flood forces to assist SPARTAN-117 and the Arbiter in preventing the Halos' activation and the Arbiter personally killed Truth. However, the Gravemind betrayed them and while Johnson managed to escape with Commander Keyes' body in the Pelican, SPARTAN-117 and the Arbiter had to fight their way outside.

343 Guilty Spark had managed to facilitate the making of a new Halo through the Ark, explaining that a tactical pulse from it would eliminate the Flood infestation. However, this new Halo lacked an Activation Index. The only way they could get another Index was to rescue Cortana from High Charity since she still possessed the Index from Installation 04. Through a tough battle, SPARTAN-117 and the Arbiter successfully entered the ruins of High Charity and recovered Cortana, using a partly-damaged Pelican to escape while High Charity was destroyed as its reactors went critical after the Master Chief blasted them.

With the Index secure, the Arbiter ordered that the remaining UNSC forces relocate to the Separatist ships and escape back through the Slipspace portal to Earth while he, SPARTAN-117 and Sergeant Major Johnson moved in on the Control Room of the incomplete Halo. The UNSC Forward Unto Dawn was left behind for them to use to escape. By now what was left of the Gravemind had relocated to the new Halo. The three heroes with 343 Guilty Spark made it through waves of Flood to the Control Room. 343 Guilty Spark explained that the new Halo would be ready to fire within days, but with Flood moving in all around them Johnson wanted to fire the ring now. When Guilty Spark protested that activating Halo now would destroy both the Ark and the installation, Johnson told him to "deal with it" and prepared to activate the ring.

Unwilling to let "his" ring be destroyed again, Spark went rampant, killing Johnson and attacking SPARTAN-117 and the Arbiter. However, by the help of a dying sgt. Johnson and his laser, SPARTAN-117 managed to destroy Guilty Spark and start the firing sequence for the new Halo. He and the Arbiter then took Johnson's Warthog and rushed towards the Dawn as the incomplete Halo powered up and started breaking apart. The two drove their way through hordes of battling Flood and Sentinel drones, with the world literally falling to pieces around them. The two heroes made it to the Dawn, where the Arbiter was almost crushed by a Battle Tank due to the sudden acceleration of the ship. Agility and a pair of crates saved him. He made his way to the bridge of Dawn and took her into Slipspace just as the new Halo fired, with Master Chief almost being crushed by the same tank which descended through the cargo hold and into space. However, the Slipspace portal collapsed as the Dawn entered it and while the forward half with the Arbiter made it to Earth, the rear half fell out of Slipspace with Cortana and SPARTAN-117 and disappeared.

With Truth dead, the Halos deactivated, and the Flood destroyed, the Battle of the Ark ended the Human-Covenant (Separatists) War. A monument was erected in New Mombasa in remembrance of those who gave their lives in the war including SPARTAN-117 who is labeled MIA. The Arbiter and his surviving brethren departed Earth for their homeworld.

Installation 00 and the Flood
It is assumed that the firing of the Halo ring either severely damaged or destroyed the Ark while killing the Flood forces around Installation 00 including the Gravemind.

Forward Unto Dawn
The portal between Installation 00 and Earth collapsed while Forward Unto Dawn was still inside it. As a result, the ship was cut in half - the front arriving at Earth and the back half being lost in space. The Arbiter, sitting on the Bridge at the time, was part of the front half but, without any engines, soon crashed. However, Spartan-117 and Cortana were in the rear half and were missing.

It is known that Cortana and Spartan-117 survived the portal's collapse. Spartan-117 went into cryofreeze while Cortana sent out a signal indicating their status. It is unknown if their message was ever received or if they were rescued, but they eventually reached an unknown planet.

Legacy
A monument was made near the Town of Voi where the Forerunner artifact had been built. It reads "In memory of those fallen in the defense of Earth and her Colonies. March 3, 2553". On it were the pictures of the most outstanding UNSC personnel who went through the portal but did not return. Spartan-117 is honored on it by a "117" scratched beside the pictures.

The Unknown
It is yet unknown, however, if all the Flood have been destroyed. There are still 5 installations that have not been found, nor is their status known. It is also not known if the Gravemind followed with all the ships in his command. There was a fleet of hundreds, if not thousands of ships around High Charity. Most of them were presumably destroyed, but there is a possibility that the ship that crash-landed near Voi was not the only ship under Flood control (a Major Elite said that the Separatists had stopped the others but that one broke through their lines and jumped to Slipspace). Additionally, the UNSC military, having barely survived a war that brought them to the brink of annihilation, are barely in a state to defend themselves, much less find and destroy the Halo rings, which means that any roving human or alien with no knowledge of the war or the rings' danger could bring the story full circle. All the Flood that escaped Installation 05 were destroyed including the Gravemind but there still may be more Flood remaining on Installation 05, although any remaining flood on the installation have no way of escaping.(It is possible to say that the Elites glassed Installation 05)  Furthermore, as the Master Chief and the Arbiter were fleeing Halo, the Gravemind claimed that this defeat would simply be "an addition of time" to a sentence it "never deserved," possibly indicating that a new Gravemind will be formed elsewhere, though it's more likely a threat than an indication of a new Gravemind.