Cortana

Cortana, UNSC AI serial number CTN 0452-9, is a "smart" AI construct, or "Intelligent Agent". She was one of the most important figures in the Human-Covenant War, and served as John-117's partner in various combat missions, as well as serving as the AI for the United Nations Space Command Halcyon-class Cruiser Pillar of Autumn and the Orbital Defense Platform Cairo Station. In addition, she held vital data pertaining to the Halos, including the Activation Index from Alpha Halo.

Creation

Cortana was created using a flash cloned copy of the famous Dr. Catherine Elizabeth Halsey's brain. Twenty flash cloned brains were created, but only one survived; it was used to create Cortana. The neural pathways of the cloned brain were scanned and copied through a process called Cognitive Impression Modeling. She is one of the only two AIs that were created from Dr. Halsey's brain, the other being her predecessor, Kalmiya another smart AI.

Cortana seems to share her creator's memories, thoughts, and even values. For example, when she was asked by Dr. Halsey to pick a "carrier", Cortana chose John-117 for their neural compatibility, and because she thought he looked good, with Dr. Halsey agreeing. She is not only a facsimile of Dr. Halsey's brain but also closely resembles her physical form, at a younger age.

Fateful Meeting

Cortana first met the Master Chief prior to the Battle of Reach, when she was integrated into his new MJOLNIR Mark V armor. Together, Cortana and the Chief passed a test that was devised by Colonel James Ackerson. The test included armed ODSTs, anti-tank mines, automatic turrets in the razor field, and even a SkyHawk for an air strike. After the test, Cortana was installed into the Pillar of Autumn for the mission she was created for. While aboard she took her revenge on Colonel Ackerson by hacking into his system and blackmailing him, hoping that this would send him back to the front lines.

Cortana's primary mission was to aid the Spartans in the infiltration of a Covenant vessel and the capturing of a Covenant Prophet. The UNSC would then try to bargain with the Covenant for a peace treaty.

The Battle of Installation 04

When the operation was canceled due to the Covenant's surprise assault on Reach, both Cortana and the Master Chief were able to fend off Covenant forces at Reach. They were eventually forced to flee the burning planet, heading to a random location as per the Cole Protocol. However, Cortana secretly inserted coordinates translated from symbols on a rock that Master Chief discovered on Sigma Octanus IV, thinking that they were of some significance to the Covenant.

After emerging out of Slipspace, the two discovered a ring shaped world called "Halo". Unfortunately, Covenant ships had followed them, and the fighting continued. Controlling the Pillar of Autumn's defenses, Cortana managed to destroy four Covenant targets over Installation 04 before the ship's weapons were disabled by Covenant boarders. Following the Cole Protocol, Captain Jacob Keyes, the ship's commanding officer, prepared to abandon ship. Because the Cole Protocol forbade the capture or destruction of any AI construct, the Master Chief was charged with protecting Cortana from the Covenant.

It was around this time that the Chief learned that Covenant forces had successfully captured Keyes and taken him to the Truth and Reconciliation. The Master Chief rescued Keyes, who left to infiltrate what appeared to be a Covenant weapons cache located in a swamp.

The Chief and Cortana used the Silent Cartographer to locate and enter Halo's Control Room, where Cortana was uploaded to Halo's core systems. When the Master Chief asked her how Halo could be used against the Covenant, she hinted that the Halo wasn't what it seemed to be. She also learned that the "weapons cache" Keyes was attacking was really a Flood Containment Facility. She stayed in Halo's systems, sending the Master Chief to find Keyes. After the Chief encountered the parasitic Flood for the first time, he was convinced by the Forerunner Monitor 343 Guilty Spark to activate the Halo.

343 Guilty Spark helped the Master Chief retrieve the Activation Index. The Chief, intent on using the Index to eliminate the Flood, returned to the Control Room and inserted the Index into the Halo's control panel. Luckily, Cortana stopped the activation sequence and removed the Index's data, informing him of the true purpose of the Halo Array. Cortana's actions saved all life in the galaxy from total annihilation. At that point, 343 Guilty Spark, seeing that the duo had no intention of returning the Index, tried and failed to kill them to retrieve it.

After enduring prolonged engagements with the Covenant and the Flood, Cortana realized that detonating the Pillar of Autumn's fusion reactors would destroy the Halo. Unfortunately, the reactors could only be activated using codes stored in the now-infected Captain Keyes's CNI. The Master Chief retrieved the CNI, and he and Cortana managed to detonate the reactors despite interference from 343 Guilty Spark. The two escaped the resulting explosion in a Longsword Fighter.

Dust and Echoes

Cortana and the Master Chief, seemingly the sole survivors of the Battle of Installation 04, discovered a small number of other UNSC personnel that had escaped the ring in a Pelican dropship. Knowing that the Pelican wasn't capable of traveling long distances, the Master Chief, along with Cortana and the Pelican's four-man crew, fought their way onto the Covenant flagship Ascendant Justice. Shortly afterward, Cortana took control of the ship, and returned the survivors to Reach, where the group helped to rescue survivors of the Second Battle of Reach.

Cortana was revealed to have taken a lot of data from Halo, and the sheer amount of information cut into her processing power and slowed her down. During her time on Ascendant Justice, Cortana exhibited uncharacteristic behavior including anger, distraction, and self doubt -- an indicator that she may have been about to enter rampancy.

It was also revealed that during Cortana's time on Ascendant Justice, she had captured a Covenant AI, decompiling the AI and copying two of its functions and gaining the ability to translate Covenant speech, and the ability to create imperfect clones of herself. These capabilities, along with her exclusive knowledge about the Halos, made her extremely valuable to the UNSC.

Ascendant Justice was effectively fused with the UNSC Gettysburg. It was at this point that Cortana learned of a planned Covenant assault on Earth. The Master Chief, along with Spartan Blue Team and an expendable clone of Cortana, would later execute Operation: FIRST STRIKE.

As it turned out, the Covenant AI that Cortana had decompiled had managed to, prior to its capture, send a message over Battlenet, warning the Covenant of its ship's capture and sending the necessary calculations for a sub-atmospheric Slipspace jump. The information was later used by the Prophet of Regret to enter Slipspace right above New Mombasa, beginning the First Battle of New Mombasa.

The Master Chief and Cortana would later return to Earth, at which point Cortana handed all of the sensitive data in her possession over to ONI.

First Battle of Earth

After returning to Earth, Cortana served on the Orbital Defense Platform Cairo, where a ceremony for both Sgt. Johnson and Miranda Keyes was soon interrupted by the arrival of a Covenant Fleet under the command of the High Prophet of Regret, starting the First Battle of Earth. Cortana was given control of the Cairo's Magnetic Accelerator Cannon to repel the invaders, and with the Master Chief's help, she successfully deactivated a Covenant bomb that would have destroyed the station. The same bomb was then used by Spartan-117 to destroy a Covenant Assault Carrier. The Chief offered for her to remain behind on the station after she said that his plan was crazy, but she chose to accompany him again, stating, "Unfortunately for us both, I like crazy." She then aided him when he arrived in New Mombasa to deal with a Scarab.

Delta Halo

Later, after escaping on-board the In Amber Clad in a Slipspace event, they discovered another ringworld, Delta Halo. Cortana gave Commander Miranda Keyes access to all information on the original Halo Ring, and provided intelligence to the Chief, UNSC Marines and the ODSTs on the surface of the ring.

After the Master Chief hunted down and killed the Prophet of Regret on Delta Halo, he and Cortana were captured by the Flood central intelligence -- the Gravemind. However, it did not harm them, instead choosing to use the two to stop the Prophet of Truth from firing the Halo. Gravemind sent the Master Chief and Cortana to the Covenant Capital Ship High Charity, where Cortana infiltrated the city's computer systems and remained there while the Master Chief followed the Prophet of Truth. She promised to detonate the crashed In Amber Clad's reactors to destroy the city and Halo if the ring was activated. However, she was left behind as a fail safe because she did not want to chance a remote detonation. As Truth boarded the Forerunner Dreadnought in the heart of the city to reach the Ark, Cortana fought with the ancient Forerunner AI Mendicant Bias to prevent the ship from launching without the Chief on board. The firing of Halo was averted by Miranda Keyes, the Arbiter, and Johnson, while the Chief successfully boarded the Dreadnought and escaped High Charity, leaving Cortana in the clutches of the true enemy, Gravemind, who had, by then, overran High Charity.

Captured

Under the control of the Gravemind and constantly being tortured, Cortana managed to send a message to the Master Chief on Earth, stashing it on an Earth-bound Flood-infected ship that crash-landed in Voi. In her message, she stated that the Gravemind was approaching Earth in High Charity, and that it was unaware of the Portal and where it lead to. On the other side, there was a solution to stop the Flood without needing to fire the remaining Halo rings; however, she couldn't give any further information, as the Gravemind might have been listening. Though Lord Hood doubted her plan, fearing it could be a Flood trap, the Chief stated that he trusts her. A joint UNSC-Covenant Separatist task force then entered the Portal, heading to Truth and to Cortana's solution.

Cortana continued to appear to the Master Chief, who successfully recovered her from the Flood Hive that was High Charity after it crashed on the Ark. Along the way, the Master Chief had several visions of her seemingly in pain. Surprised that the Chief had against all odds rescued her as he promised after the First Battle of High Charity, as well as being surprised that Thel 'Vadam and Chief "made nice", Cortana managed to gather herself and produce the Index from Installation 04, which she had kept. With it, Cortana was able to activate the newly constructed Installation 04, which fired prematurely and destroyed itself and The Ark along with it.

End of Halo 3

The Slipspace portal collapsed as the Master Chief, Thel 'Vadam, and Cortana attempted to escape through it, cutting the UNSC Forward Unto Dawn in half. While 'Vadam, who was on the bridge, managed to return to Earth safely, the Chief and Cortana, who were in the hangar, were left drifting in space. Cortana activated a distress beacon, but knew that it could be days, years even, before they were found. As the Master Chief prepared to go into a cryogenic sleep to await rescue, Cortana confessed to him that she would miss him. They were last seen drifting towards an unidentifiable object.

  "I'll miss you."
  —Cortana