The following occurs directly after the events in Halo: Uprising. Background: The Covenant currently occupies Earth, and is amassed at an excavation of an artifact of Forerunner origin.
It is a night sky: several bright pinpoints of white lights hang in the center. It's a tranquil forest, with lust forestry and a winding river. A fireball hurtles through the sky. Then, Cortana's voice begins whispering:
Cortana: "They let me pick. Did I ever tell you that? Choose whichever Spartan I wanted. You know me. I did my research. Watched as you became the soldier we needed you to be. Like the others, you were strong and swift and brave. A natural leader. But you had something they didn't. Something no one saw... but me. Can you guess? Luck. Was I wrong?"
Sergeant Major Johnson and his squad find the Master Chief lying on the jungle ground after having fallen through the atmosphere. It seems that the Chiefs armor is in partial lockdown, with its owner unconscious. Just as the Sergeant radios for extraction, Master Chief surprises the squad by regaining consciousness. Johnson rebukes the Chief, saying, "You crazy fool, why do you always jump? One day you're going to land on something as stubborn as you are!" After a quick systems check, the Marines and their new found ally, the Arbiter, head out towards the river for evac. They reach the river and the Pelicans, but before they are able to board, the drop ships are attacked by Banshees. Johnson and his squad disappear in the ensuing chaos and are presumably captured. It is now up to the Chief and the Arbiter to rescue him. They eventually come across an UNSC outpost, which has been taken over by the Covenant. Both the Chief and the Arbiter push though waves of enemy to take back the outpost and rescue the captured Marines. Their victory is short lived, however; only moments after the fight, Covenant reinforcements arrive and the outpost falls under attack once again. Just as it seems like they are about to be overrun, Pelicans arrive and spray the Covenant ranks with missiles.
The Pelicans bring the Chief, Arbiter, Johnson and his squad to a concealed base deep in the jungle. Master Chief meets up with Commander Miranda Keyes in the Ops Center, and they begin to discuss tactics with Admiral Hood. With only a few ships left, the Admiral has little choice but to throw everything he has at the remaining Covenant hovering over the artifact. However, to do so, the Chief has to clear all anti-aircraft batteries from the city of Voi. Halfway through the discussion, the transmission is interrupted by the Prophet of Truth, who claims that Earth will "burn until its surface is but glass", and that not even "the demon" will survive. Realizing that an attack is imminent, Keyes orders an evacuation, telling all able bodied Marines to prepare to fight. The Covenant begin to invade the bunkers, so the Master Chief and the Arbiter set off to repel the enemy while Johnson and his squad set up a bomb to destroy the base- and the invaders. Halfway through the battle, Johnson is driven out of the Ops Center by Brutes. The Chief is forced to return to the Ops Center and rearm the bomb, and then make a speedy getaway via the elevator in the hangar.
Following the plan of attack outlined by Lord Hood, the Master Chief must clear a path into the city of Voi. Using spare Warthogs from the barracks, the Chief, Arbiter, and some Marines fight their way through the Tsavo Highway. After several moments of high-speed travel and copious amounts of fighting, the team comes across a destroyed section of the highway and must continue on foot. This is hardly a favorable circumstance for the Marines, as they are massively outnumbered by the Covenant. The Chief is forced to fight through waves of Brutes on foot while waiting for re-supplies. Eventually, a Pelican circles ahead and drops some supplies as well as a Warthog. They finally reach the end of the highway and encounter a gigantic Brute barricade, complete with energy barriers, turrets, and several Wraiths. Taking out the Brutes one by one, the Chief and the Arbiter finally are able to destroy the barrier blocking the tunnel and drive through.
Having reached the outskirts of Voi, the team comes across the first anti-aircraft battery. It just so happens that the entire area is swarming with Ghosts and Wraiths, giving the Chief and the Arbiter no choice but to jump into battle. The field turns into general pandemonium as explosions blow craters into the ground and vehicles explode into blue flames. Eventually, all anti-aircraft batteries are neutralized... but a scout report tells the Chief that "something big is on its way." A Scarab suddenly looms overhead, firing beams of plasma at the Marines. Master Chief boards the Scarab and, with a few well placed rockets to the power core, destroys the walking tank. With the Scarab out of the way, the Chief and the Arbiter receive orders to take out the anti-aircraft cannon in the vicinity. They head in that direction, rescuing several workers and killing a pair of hunters. They reach the heavily guarded cannon and take out all the opposition. Again, a few well placed shots into the core of the cannon destroy it, rendering the skies clear for an aerial assault on the Covenant war ships. MAC cannons boom as Human gun ships open fire on the Covenant, while the Chief and the Arbiter watch. But the attack is cut short by the abrupt activation of the artifact. Blown back by the shock wave, the Chief and the Arbiter rise to their feet to witness the Covenant ships entering into a gigantic, stable slipspace portal. As the Human ships are recovering from the shock wave, another, smaller slipspace portal opens and a Flood-controlled Covenant ship crash-lands nearby:
Arbiter: What is it? More Brutes?
The Flood immediately begins to spread though the city and hoards of combat forms attack all that move. The Elites begin to deploy drop pods to help manage the outbreak, and tip off the Master Chief that Cortana may be somewhere in the ship. The Chief wades through the sea of zombies and manages to get inside. He locates a memory module only to meet 343 Guilty Spark, who insists on transporting the module for safekeeping and repairs. Recalling the events on the first Halo where Guilty spark tried to kill him, he reluctantly lets Spark carry it. The Master Chief escapes the ship, and the Elites proceed to glass the continent in order to contain the Flood. They regroup in the Elite carrier Shadow of Intent, high above Voi, where Guilty Spark manages to repair the module and deliver Cortanas disturbing message:
Cortana: High Charity... the Prophets' holy city, is on its way to Earth, with an army of Flood. I can't tell you everything. It's not safe. The Gravemind... it knows I'm in the system. But it doesn't know about the Portal, where it leads. On the other side, there's a solution; a way to stop the Flood, without firing the remaining Halo rings. Hurry, Chief! The Ark... there isn't much time.
Master Chief insists on following Cortanas advice against a reluctant Admiral Hood. Both fleets prepare themselves and follow the Covenant through the portal.
The fleet exits slipspace at the Ark, which is surrounded by the Covenant fleet. The Elite fleet engages the Covenant while Pelicans filled with ODSTs, the Chief, and the Arbiter stream towards the Ark. Upon landing on the surface, Guilty Spark announces that the Prophet of Truth has barricaded himself in the core of the facility and has activated a barrier around it. Destroying the generators will drop a portion of the shield, and allow the Marines and the Elites to punch through. Johnson heads towards the third generator, the Elites go to the second and the Chief and the Arbiter fly to the first. Master Chief is gazing out of the back of the Pelican when all of a sudden the rear Pelican bursts into flames. The entire fleet goes down, destroying lots of supplies and the only Warthog. The Marines are forced to destroy the anti-aircraft batteries before re-supplying, rushing to the tower and disabling the generator. The Elites turn off the second generator immediately after. Everyone turns to observe the final tower, but it does not turn off:
Johnson: "Brute reinforcements, ma'am. We're pinned down!"
Miranda Keyes: "I'm on my way!"
Johnson: "Negative! Fire's too heavy! Everyone fall back! Now! (Static and cut-off)
Miranda Keyes: "Sergeant Major?! Johnson?! Can you hear me?!
The Marines mobilize on the beach for an assault on the third tower. Master Chief climbs into a Hornet attack craft and escorts the Pelicans and Phantoms to the generator. After taking out several anti-air batteries and enemy Phantoms, the troops drop off on the towers platform. Fighting through the entire building, they finally reach the top and shut off the generator. As Shadow of Intent begins its bombardment of the core, the now Flood city of High Charity shoots out of a slipspace portal, showering the area with debris. Shadow of Intent is shredded by this shrapnel, which render its weapons systems useless. Moreover, the Flood is now outside of the galactic target area; the Halos wont stop them anymore. Dispatching the local Flood threat, the Chief regroups with the rest. A quick journey by Hornet, interrupted only by two Scarabs, brings Master Chief, the Arbiter, the Elites and the Marines into the core of the Ark.
As the Chief and the Arbiter rush as quickly as they can to the top, Sergeant Johnson is being beaten by his Brute captives. Seeing as how the Prophet of Truth is about to use Johnson to activate the rings and Master Chief isn't anywhere near the top, Miranda Keyes crashes a Pelican through the upper window. She is quickly outnumbered however, and reaches a mutual understanding with Johnson. She needs to kill them both so none of them can be used to activate the rings. Just as she is about to shoot Johnson, she makes eye contact with him and hesitates- then falls to the ground, dead, her back riddled with spikes. The Prophet drops his spiker with disdain:
Truth: "Your forefathers wisely set aside their compassion... Steeled themselves for what needed to be done... I see now why they left you behind. You were weak, and Gods must be strong."
Truth grabs Johnsons hand and forces it on the activation button. Instantly the Control Terminal begins to change and seven holographic halo rings light up one by one. At the end of the corridor, the Chief and Arbiter emerge from the lift just in time to witness the activation. As they are about to rush in, two pure Flood tank forms drop from above:
Flood: "Do not shoot, but listen! Let me lead you safely to our foe. Only you can halt what he has set in motion!"
The unlikely union of Flood, Human, and Elite rush down the corridor to Truth. With flood forms swarming over every inch of the terminal and the combined efforts of the Chief and the Arbiter, all Brute opposition is quickly put down and the Prophet cornered. Truth continues to spew his religious speech even when threatened at sword point, declaring at the end that he is "the voice of the Covenant." The Arbiter retorts that because Truth is the voice, he must be silenced, and plunges his sword through Truth. As the Prophet crumples to the ground, a sinister laugh echoes through the facility and the Flood forms turn to face the Chief and the Arbiter. "We trade one villain for another," the Arbiter observes. Johnson rushes to the Pelican with Keyes's body and starts to fly the ship out. Master Chief and the Arbiter try to grab hold but are knocked off Flood forms. They fight their way back to the lift and upon finding it broken, jump down the dark shaft.
The room is dark, with exposed wiring lighting up the area in intervals with a shower of sparks. They are scanning the room for hostiles when a purple flicker catches Master Chiefs eye. He jumps up and chases it around the corner. The purple flicker forms into an image of Cortana, which keeps on walking. Chief follows the image of Cortana until it stops at a panel. He presses the button and an observation panel opens up to reveal a giant, incomplete Halo rising out of the fog:
Arbiter: A replacement. For the ring you destroyed
Master Chief: (To Guilty Spark) "When did you know?"
343 Guilty Spark: "Just now. But I had my hopes. What will you do?"
Master Chief: "Light it."
343 Guilty Spark: "Then we are agreed! A tactical pulse will completely eradicate the local infestation! I will personally oversee the final preparations. Though it will take time to fabricate an activation index."
Arbiter: "How will you light it?"
The Chief turns and looks at High Charity, deep in thought.
Two banshees land gingerly on the floor of the Flood hive, the former Covenant holy city of High Charity. The Chief and the Arbiter dismount. The entire city is built out of organic material that squishes under boot; gaping, pulsing, oozing orifices and corridors reminiscent of the inside of an intestine. Master Chief and the Arbiter do little more than shoot Flood forms while rushing to find Cortana. Along they way, they are assaulted with transmissions from a tortured Cortana and an aggravated Gravemind:
Gravemind: "Child of my enemy, why have you come? I offer no forgiveness... For a father's sins are passed to his son. Of course, you came for her. But we exist together now. Two corpses in one grave."
Cortana: "A collection of lies; that's all I am! Stolen thoughts and memories!"
Cortana: "It was the coin's fault!* I wanted to make you strong, keep you safe. I'm sorry, I can't."
Cortana: "What's your name? It's very nice to meet you. You like games? So do I."*
Cortana: "I'm just my Mother's shadow... don't look at me, don't listen! I'm not what I used to be..." *
Gravemind: "Time has taught me PATIENCE. But basking in new freedom, I will know ALL THAT I POSSESS!"
Cortana: "I have walked the edge of the abyss. I have seen the future. And I have learned. There will be no more sadness. No more anger. No more envy."
Gravemind: "SUBMIT! END HER TORMENT AND MY OWN! You will show me what she hides! Or I shall feast upon your BONES!!"
The Chief begins to reach the end of the hallway.
Cortana: "This is UNSC AI Serial Number CTN0452-9. I am a monument to all your sins."
The Chief rushes to the end of the hallway, to find Cortana in a Stasis Shield in on of the panels in the room. He beats and bashes the shield until it finally breaks. On a holographic projector lies Cortana. Master Chief tells Cortana that when he makes a promise, he keeps it; referring to Halo 2 where he promised to return for her. She slowly gets up, recovering her strength and presenting the Chief with the activation index from Installation 04. Asking him how he was going to get out, the Chief responds, saying "Thought I'd try shooting my way out, mix things up a little." He then inserts Cortana into his armor. As they head out, Cortana remarks with tenderness, "Just keep your head down, there's two of us in here now, remember."**
Cortana advises that they destroy High Charity. With practiced ease, Master Chief takes out the reactors and sends them into critical meltdown. Running and gunning, they make it to a downed Pelican and board. With Flood tentacles clawing at the ship and explosions rocking it back and forth, they craft struggles for every bit of altitude. They just barely escape a massive explosion, and head towards the new Halo ring.
*These lines refer to the prequel, The Fall of Reach. The coin and the game is a test that Dr. Halsey performed with John 117 as a small boy. She would flip the coin and John would demonstrate his incredible ability of always winning (or luck); he is able to discern what side of the coin would land on top when it was flipping too fast to have possibly been seen. Cortana is an imprint of Dr. Halsey, a collection of her brainwaves and personality.
**This is the line of dialogue spoken by Cortana in Halo: Combat Evolved when you loose your first health bar in combat. She speaks it with rebuke in Halo 1, and with nostalgic love in Halo 3.
The Pelican crash lands into a snowy bank, revealing an area that looks remarkably like the control room from Combat Evolved. Sergeant Johnson is bringing the frigate Forward unto Dawn closer to the control room for their escape strategy. Gravemind has more than half a mind to stop them, however, and sends waves of dispersal pods at them. With Flood forms rushing up at them from every direction, the Chief and the Arbiter haul as fast as they can to the control room, with Johnson providing cover with a spartan laser. They reach the top and Guilty Spark opens the door for them, shutting them just in time to block the Flood. Guilty Spark excitedly explains that the ring would be ready to fire in a few days. Its incompletion renders its destruction imminent should it be fired now, but of course, thats what the Chief needs. Upon hearing this, Guilty Spark goes crazy and attacks Johnson, Master Chief, and the Arbiter. Spark reveals a bit of Forerunner history at this point, saying "You are the child of my makers. Inheritor of all they left behind. You are Forerunner. But this ring is mine!"
The armor of Master Chief and the Arbiter disperse most of Guilty Sparks energy, but it cuts straight through Johnson's ballistic armor. Master Chief opens fire on Guilty Spark, and watches as his bullets ping off Spark uselessly. Suddenly, a laser beam lances through the air and Spark is blasted across the room. A mortally wounded Johnson hands an overheated Spartan laser to Master Chief, telling him to kick Sparks ass. Several shots from the Spartan laser later and Spark explodes in a shower of... sparks. Master Chief tries to revive Johnson, but it is clear that he is dieing. Johnson tells chief to keep Cortana with him always, and to "never let her go... send me out with a bang." Cortana activates the ring, and everyone runs back outside. Getting into the Warthog that Johnson used to get here, they speed away with Halo crumbling around them.* The Warthog just barely makes a jump into the hangar of the frigate Forward unto Dawn as the Installation crumbles around them. The Chief inserts Cortana into the ship as Scorpions, Warthogs, and supply boxes are sucked out by the explosion. The frigate begins to lift off into the portal when a Warthog clips the Chief, and he starts to fly out. He punches a handhold for himself into the floor, and slowly is able to crawl back into the hangar and take refuge behind a pillar:
Cortana: "If we don't make it..."
Master Chief: "We'll make it."
Cortana: "It's been an honor serving with you, John."
The Installation fires and subsequently explodes, and everything goes blank.
*This is a remake of the last level in Combat Evolved.
The front end of the Dawn crash lands into an ocean on earth. Rescue workers recover the half ship and pull the Arbiter from the wreckage. There is no sign of the Chief. After several days, a memorial service is held for those fallen in the war:
Admiral Hood: "For us, the storm has passed. The war is over. But let us never forget, those who journeyed into the howling dark and did not return. For their decision required courage beyond measure, sacrifice, and unshakable conviction that their fight; our fight, was elsewhere. As we start to rebuild, this hillside will remain barren, a memorial to heroes fallen. They ennobled all of us, and they shall not be forgotten."
Admiral Hood: "I remember how this war started. What your kind did to mine. I can't forgive you. But...you have my thanks, for standing by him to the end."
The Arbiter shakes Admiral Hood's hand.
Admiral Hood: "Hard to believe he's dead."
Arbiter: "Were it so easy."
The Arbiter leaves the Memorial. His Phantom heads back to the Shadow of Intent, hovering above. The Arbiter meets Shipmaster Rtas 'Vadum on the bridge, looking at a holographic image of Earth:
Shipmaster Rtas 'Vadum: "Things look different. Without the Prophets' lies clouding my vision. I would like to see our own world. To know that it is safe."
Arbiter: "Fear not. For we have made it so."
The Arbiter clenches a fist to his chest.
Shipmaster Rtas 'Vadum: "By your word, Arbiter."
Arbiter: "Take us home."
The Shadow of Intent leaves Planet Earth. Going back to the memorial, underneath the print "UNSCDF March 3 2553", the numbers "117" are scratched in, to dedicate to the Master Chief, who had no picture, or belongings to be remembered by.
(After the credits, deep in space) The back half of the Dawn is floating deeper into unexplored space:
Cortana: "Chief? Can you hear me? I thought I lost you too."
Master Chief: "What happened?"
Cortana: "I'm not sure. When Halo fired, it shook itself to pieces. Did a number on the Ark. The Portal couldn't sustain itself. We made it through just as it collapsed. Well... some of us made it. But you did it. Truth and the Covenant. The Flood (she's plugged into the panel and appears). It's finished."
Master Chief: "It's finished."
Cortana: "I'll drop a beacon. But it'll be a while before anyone finds us (The Chief places himself in one of the Cryotubes). Years even... Ill miss you."
Master Chief: "Wake me. When you need me."
Cortana smiles. The Cryotube seals, freezing the Chief.
Legendary Segment: The back half of the Forward Unto Dawn is seen drifting to the night side of an unknown planet. The sun suddenly shines onto the planet, chasing away the dark and revealing the Marathon symbol on the planet side.