I and a lot of other people in the Halo fandom have formed the theory that in Halo 5, Cortana has the logic plague, and that the flood drives her actions throughout said game.
During the events of Halo 2 and the first half of Halo 3, Cortana was engaged in a month-long conversation with the current Gravemind at the time, this should be more than enough time for the Gravemind to infect her and/or plant the seeds for it to appear later in her lifetime. The same thing happened to 032 Mendicant Bias during the Forerunner-Flood war while he was interrogating the Gravemind at the time, The Primordial, and seeing as Mendicant was a far more advanced AI, a Gravemind with more intelligence than The Primordial should easily be able to infect Cortana in the time that they had.
It is also heavily hinted at in one of the Halo Loot Crate Data Drop: Data Drop: Subject Denver
As seen in Awakening the Nightmare, it is revealed that the flood survived the Battle Of The Ark, and due to the present of Flood Pure Forms, a new Gravemind must have formed/the Gravemind we all know and love survived. Because of this, Cortana would have a substantial enough Flood force to attack Humanity.
During the events of Halo 2 and the first half of Halo 3, Cortana was engaged in a month-long conversation with the current Gravemind at the time, this should be more than enough time for the Gravemind to infect her and/or plant the seeds for it to appear later in her lifetime. The same thing happened to 032 Mendicant Bias during the Forerunner-Flood war while he was interrogating the Gravemind at the time, The Primordial, and seeing as Mendicant was a far more advanced AI, a Gravemind with more intelligence than The Primordial should easily be able to infect Cortana in the time that they had.
It is also heavily hinted at in one of the Halo Loot Crate Data Drop: Data Drop: Subject Denver
As seen in Awakening the Nightmare, it is revealed that the flood survived the Battle Of The Ark, and due to the present of Flood Pure Forms, a new Gravemind must have formed/the Gravemind we all know and love survived. Because of this, Cortana would have a substantial enough Flood force to attack Humanity.