Halo 2: The Story
Picking up from where Halo: Combat Evolved left off, the Master Chief and Cortana are floating in space with the debris from the destroyed Halo-04. Full-to-the-brim with valuable intel and a handful of surprise survivors rescued from the destruction of the Halo construct (among them Sergeant Avery Johnson, the only man who survived Flood infection), the Chief plans to return to Earth and eventually do by boarding a Covenant flagship, Ascendant Justice.
Once they get most of the ship secured, the small group humans decide to return to Earth with accounts of what happened on Halo-04 and for the first time in UNSC history, a captured Covenant warship. This kind of technology for the human race would help them to win the war. Ascendant Justice's first jump is back to what's left of the planet Reach, still in line with the Cole Protocol. Because the Protocol dictates that a captured Covenant vessel must be searched and stripped of all tracking devices before going to Earth, the short-handed crew decides to leave the Ascendant Justice in orbit around Reach and return to Earth using a human warship. The Master Chief however has one more reason for visiting Reach: as the SPARTANs commanding officer, he is saddened by the orders he gave his team, which he now feels were something of a death sentence. The Master Chief wants to search Reach, seeking a closure or even better, survivors.
Upon arrival in Reach's star system, the Ascendant Justice's crew picks up a signal from a handful of UNSC survivors, including a few SPARTANs and Vice Admiral Danforth Whitcomb, the Deputy Chief of Naval Operations, who has armed an anti-planet "Nova" nuclear mine, a weapon that will turn Reach, as well as the Covenant invasion force, into dust. While investigating on Reach, the Chief also discovers Dr. Catherine Elizabeth Halsey and the rest of the living SPARTANs have obtained a Forerunner artifact, which appears to have bent time so that the Chief and Cortana could rescue Halsey and the others. While all this is going on planetside, Cortana finds out that the Covenant have discovered the location of Earth, which they don't really know is Earth, and are about to deploy a large strike fleet.
The humans then fend off multiple attacks from the Covenant, who are determined to retrieve the Forerunners' relic in the SPARTANs' possession. Seeking a safe place to conduct repairs on Ascendant Justice, the UNSC forces join with the rebels of the Eridanus asteroid field. While docked at the rebel base, Dr. Halsey sedates SPARTAN Kelly-087 and takes her on a personal mission, location unknown.
With the knowledge that the Covenant are en route to Earth, the Master Chief and his SPARTANs, determined to buy some time, decide to go to the enemy fleet's rendezvous point and disrupt its preperations in a decisive "first strike". The SPARTANs successfully infiltrate the Covenant command and control center station, named the Unyielding Hierophant, and with Cortana's help they are able to set it for self-destruction. In spite of this effort, and Grace-093 KIA (see SPARTAN roster), the Covenant forces are not yet crippled, but Admiral Whitcomb manages to trick all of them to follow Ascendant Justice near the doomed space station, pretending the Forerunners' artifact from Reach is aboard his ship. A few minutes later the Unyielding Hierophant blows up, obliterating almost the entire Covenant fleet (over 500 ships destroyed), but in the process the Admiral is killed and Ascendant Justice destroyed. Onboard a damaged UNSC frigate, the Gettysburg, John-117 and the surviving SPARTANs, along with Sgt. Johnson and Cortana, head back to Earth to warn the UNSC of the Covenant's upcoming invasion.
Below section taken from Wiki
Halo 2 opens with Master Chief receiving an award aboard Cairo Station, a MAC gun platform orbiting Earth, alongside Miranda Keyes. Miranda is the daughter of Captain Keyes, who died during the course of Halo: Combat Evolved, and Miranda is accepting a posthumous award for her father's bravery. This ceremony is juxtaposed with the judgment and torture of the former Elite admiral of the Covenant fleet Particular Justice, who is being punished for his incompetence. Both events are in response to the destruction of Halo during the events of Halo: Combat Evolved. Master Chief is awarded for his bravery and sacrifice, and the unnamed Covenant admiral is being tortured for his inability to prevent the destruction of Halo. It is also revealed that the Covenant's interest in Halo lies in the belief that the activation of Halo would bring about the "Great Journey", which would cleanse the universe of lesser lifeforms (including the Flood) while providing salvation for the Covenant.
The action begins following the Master Chief's ceremony. A Covenant fleet jumps out of slipspace near Earth and sends boarding parties towards a battlecluster of stations. These boarding parties are secretly carrying explosives designed to take out the MAC (Magnetic Accelerator Cannon) guns. Master Chief finds and disarms a bomb located on Cairo Station with the help of Cortana, while the flagship of the Covenant fleet speeds past Earth's defenses and heads toward Earth itself. Master Chief and Cortana join the UNSC ship In Amber Clad, which is en route to New Mombasa to deal with the Covenant flagship. In Amber Clad is carrying Staff Sargeant Johnson, and is piloted by Miranda Keyes.
Before reaching New Mombasa, Cortana decodes transmissions revealing that the flagship carries the High Prophet of Regret. The UNSC successfully repels the Covenant invasion force with the help of Master Chief, and the Covenant ship begins preparations for a slipspace jump to an unknown destination. In Amber Clad follows, and discovers a second Halo installation dubbed "Delta Halo". The crew of In Amber Clad learn more about the Covenant's belief regarding the Halos, and Master Chief ultimately slays the High Prophet of Regret while attempting to prevent the activation of Delta Halo.
The action switches to the condemned Covenant fleet commander assuming the role of the Arbiter. His first mission is to silence a heretic who doubts the Prophets' teachings, in turn starting the Arbiter along a path which ultimately results in Arbiter doubting his own beliefs. Seeds of discord are further sown within the Covenant when the Prophets decide to grant the Brutes control of the military instead of the traditionally favored Elites. During his missions, The Arbiter realizes the danger that the rings represent: they are weapons designed to destroy most of the life in the galaxy, not the religious artifacts the Covenant believes them to be.
The Master Chief and the Arbiter meet upon the release of the Flood from Delta Halo. A mysterious Flood creature called the Gravemind sends the Arbiter and Master Chief in separate directions to prevent The High Prophets from activating Delta Halo. Master Chief finds himself aboard the Covenant Holy City High Charity, a gargantuan space station, and pursues the remaining Prophets. During Chief's mission, he finds himself in the middle of an erupting Covenant civil war between Brutes and Elites. After capturing the In Amber Clad, the Flood, led by the Gravemind, arrive at the city and begin to consume and infect the populace. The only remaining High Prophet, Truth, escapes on a Forerunner vessel hidden in the core of High Charity. The Master Chief manages to stow away on board while Cortana stays behind in order to detonate the In Amber Clad's engine reactors to destroy Delta Halo and High Charity, stopping Tartarus from activating Halo.
The game comes to a close with The Arbiter's missions as he is aided by a group of Elites as well as surviving members of In Amber Clad's crew. Together, they pursue and kill Tartarus and his Brutes on Delta Halo. Tartarus, however, has already succeeded in inserting the Index, making Delta Halo fully operational. Miranda Keyes manages to snatch the Index out of Delta Halo's control panel, thus halting the firing sequence. Despite this success, Delta Halo's deactivation sends a signal out to the other Halos, sending them all into a "standby" mode so they can be remotely detonated from the Ark. Meanwhile, the Forerunner ship that Master Chief has stowed away on approaches Earth. One of Earth's remaining orbital forces contacts him and asks what he is doing aboard the Forerunner ship. He replies, "Sir, finishing this fight," ending the game on an abrupt cliffhanger, and setting the tone for Halo 3.
After the game credits finish rolling, a scene appears in which Cortana and Gravemind are conversing. This is meant as a further teaser for Halo 3.
