Master Chief and Cortana are trapped in space onboard a human spacecraft salvaged from the Pillar of Autumn prior to it being obliterated into a million pieces. Several long days have gone by since the crew's landing on Halo. Cortana homes in on a remaining human carrier ship alone in the mass devastation left by the explosion. The two ships attack a Covenant ship and then dock together after winning. Sergeant Johnson, the only soldier that made it out of the battle facility, steps out of the drop ship and greets Master Chief. After discussing rich and valuable information about the flood and the covenant, Master Chief and Johnson decide to attack the Covenant flagship.
They launch there attack on the Covenant spacecraft. As soon as they breach the ship's exterior, Cortana hacks her way into the central control system and kills the Covenant by means of poison gas. After eliminating the Covenant threat, the ship makes a jump through hyper space and arrives at Reach. Master Chief then removed all possible tracking devices and methods from ships body to ensure that they would not be followed. He also left the ship and searched for survivors; maybe he could find a remaining Spartan.
The crew of the pirated Covenant ship mach all the way to a human base. Here, they plan a last stand against the Covenant forces to stop their dictator, the Hierarch Prophet of Truth. Truth is desperately trying to initialize an artifact located in Kenya. John is assigned a mission in where he must lead the human to Voi, a UNSC base. Manipulating Chief's attack, Admiral Hood begins his attack against the Covenants, but they escape by activating a gateway to a different world. The UNSC forces have no clue on what's going on and a ship full of infective flood lands on Earth. The Arbiter and the recently seceded Elites help against the flood by melting the Earth's surface and turning it in to glass. Master Chief then rallies his troops as they embark on an adventure through the recently created portal. With them is the robot found on the original Halo, 343 Guilty Spark. He concludes that with his advice and guidance, Master Chief can succeed in his annihilation of the Prophet of Truth.
Master Chief has arrived at the Forerunner base, the Ark. Here, Truth and his Covenant forces look to activate all existing Halos in order to eliminate the flood threat and begin there religious “Great Journey”. Little does he know that by using the Ark's mighty power, he will doom his race and everything else within a three galactic radii. The annoying little artificial intelligence, 343, secretly is informed that the original Halo is being rebuilt. This little information convinces him to aid Master Chief so he can return to his home world. The Arbiter and John 117 maneuver their way to the Ark's control room with the help of a surprisingly helpful Guilty Spark.
Aboard the Covenant flagship, the parasitic flood arrive at the Ark in search of food to feed there eternal crave. The Prophet of Truth ambushes the group and imprisons Sergeant Johnson. Master Chief rendezvous with Truth and a massive battle ensues. The humans are victorious but lose a leading officer, Miranda Keyes. Truth knows he is defeated but still roars his commands to the futile Covenant. The Arbiter sneaks up on him and ends his life with an energy sword to the throat. John 117 uses the reconstruction of the original Halo to his advantage. He believes he can destroy the immediate flood by firing its weapon and blowing up the Ark. He then remembers that you must have an activation index to fire the destructive beam from a Halo ring. Cortana is the only thing with it so he must rescue her from the Covenant flagship, the High Charity.
When they land on the reconstructing Halo, they find traces of a flood entity trying to rehabilitate itself. Infuriated, 343 warns John 117 that firing Halo's weapon would destroy the Ark and that they would all be doomed. John replies, “Shut up, Sparky” (Nylund 372). While he attempts to initialize Halo's weapon, 343 goes crazy and gets killed by Master Chief. They all barely manage to evade Halo's blast as they hurl their ship into space clinging on for dear life.
Their ship crash lands onto Earth and people believe that there were no survivors. The Arbiter steps out and gives praise to his fallen comrade, John. He leads a procession where they honor and remember the many fatalities of the war and the loss of a very dear friend. Master Chief's days of onslaught against the Covenant are over; he has perished. Later on, Arbiter and his fellow elite soldiers embark for there home world to finally live in peace and not be terrorized by the Prophets.
Showing patriotism can mean anything from wearing your area's colors, or even voting. Bungie took Master Chief's portrayal of patriotism over the limit, elevating him to superhero status. The green-tint of his MJOLNIR Mark VI armor increases his ideal of drive for his planet. Green stands for ambition and self-respect. Master Chief John 117 uses this ambition to provide a punishing boost when pulverizing puny aliens. His orange polarized visor ties in perfectly with John 117's mindset. The orange stands for vitality through endurance which describes Master Chief very well. Master Chief never dies.
