Halsey cloned her own brain to create Cortana, and so Cortana herself is a clone of Halsey. Halsey also has a close relationship with her Spartans, shown by her close friendship with Johnny and the respect Jorgey had for her.
Halsey reverse-engineered Forerunner technology to create the Infinity, but during a visit to the Infinity by Halsey as it was orbiting Requiem she decided to ally herself with Jul Mdama and his cultist gang in order to learn more about the Forerunners. ONI saw this as a big crime, simply because they didn't like Jul, and order one of the Annoying Female Associates to take Halsey out. Commander Awesome, however, decided this was wrong, since he has sense, and this massive battle took place between the Spartans over whether Halsey should or should not be killed.
Meanwhile, Halsey discovered the Librarian's hologram which gave her a key to unlock all the Forerunner Installations throughout the Galaxy. However, Jul took one half of the key and Halsey threw the other half to the approaching team of Spartans when they arrived. The Spartan team leader shot Halsey in the arm as the others tried to save her, leading Halsey to believe that the entire squad had been sent to kill her. After losing her arm, Halsey vowed to take revenge on the UNSC.
Despite her pledge, Halsey's faith in Jul appeared to wane over the coming year. She apparently abandoned her desire for revenge when she realised that her AI daughter Cortana was still alive, and had conquered the Forerunner world of Genesis and was summoning Guardians to aid her in taking over the universe - Halsey then notified the UNSC who sent a gang to kill Jul and rescue Halsey.
Halsey travelled to Sanghelios with her new chums to help deliver Fireteam Osiris to Genesis. Sarah Palmer and Halsey seemed to set aside their differences and team up to get Osiris where they needed to be, whilst also aiding Arbiter in his war against the Covenant.
Meanwhile, Johnny's attempts to save Cortana are made even more complicated...