How Cortana Is Created In Halo: Origin & Flash Cloning Explained
This article contains spoilers for Halo episode 2.
The AI named Cortana is one of the most important characters in Halo, and the TV show is adapting her creation in a remarkably faithful way. When gamers were introduced to the Master Chief back in 2001's Halo: Combat Evolved, he essentially came as part of a package deal; an artificial intelligence named Cortana was plugged into his systems, serving as a crucial adviser and an asset as he explored an ancient Halo Ring. Over the years, Cortana would develop into a three-dimensional character in her own right - although she wouldn't remain an ally for the Master Chief.
Cortana is an incredibly intelligent smart AI, whose data chip can be transferred between different systems - meaning she can pilot a starship, cooperate with John-117's Mjolnir armor, infiltrate a Covenant network, or even get plugged into Forerunner networks. Like all smart AIs, in the main Halo timeline Cortana has a limited lifespan before her coding begins to break down and she goes insane - a fate referred to as "rampancy." Sadly, Cortana's rampancy is accelerated by the sheer amount of data she absorbs from interaction with Covenant and Forerunner technology.
Cortana is as important a character to Halo as the Master Chief himself. She's yet to really make her presence felt in Paramount+'s Halo TV series, though, because season 1 feels like something of an origin story; Dr. Halsey is still conducting illegal and unethical experiments that will ultimately lead to Cortana's creation. But, although Dr. Halsey's process seems remarkably faithful to the original canon, there are hints this version of Cortana will be a little different.
In the original Halo game timeline, Cortana is a unique AI based on Dr. Halsey - the creator of the Spartan program - herself. Dr. Halsey may be one of the UNSC's greatest scientists, but she's also thoroughly egotistical, and naturally she became interested in the idea of creating an AI based on her own brain patterns. This is possible using a technique called Cognitive Impression Modelling, which conducts deep scans of a so-called "donor" brain to create an AI according to its patterns. Unfortunately, CIM is a dangerous process, because it destroys the donor brain. Halsey was, naturally, unwilling to die in order to create Cortana.
So Dr. Halsey took another approach, creating an illegal flash clone of herself. Flash clones are exact duplicates of a living human being, even retaining the memories of the original. Sadly, such duplicates have only a limited lifespan, their bodies breaking down over the course of six months to a year. Dr. Halsey had already mastered flash cloning as part of her controversial Spartan program, because she'd kidnapped potential recruits as children and replaced them with flash clones so the parents wouldn't know what had happened. Halsey created more than 20 AIs based on flash clones, but only two were successful - Cortana, and her predecessor Kalmiya.
The Halo TV series is, for the most part, remarkably accurate to the wider Halo franchise's lore; there is, however, one significant difference. In the main Halo timeline, smart AIs are fairly commonplace, with many coordinating UNSC bases such as Reach or running spaceships. Even Insurrectionists used smart AI, with one responsible for maintaining the Rubble, controlling the movement of its many asteroids to sustain it. In contrast, in the Halo TV series smart AIs don't appear to exist yet; it looks as though Spartan creator Dr. Halsey is a pioneer in this field, who wrote a paper suggesting a smart AI could be created by duplicating the brain patterns of a person via flash cloning. The Halo TV show's Cortana will therefore be the first of her kind, and possibly the only smart AI seen in the entire show. It means her existence will be even more isolated - but it also means the UNSC won't know what to expect from her. She may not even know there is the possibility absorbing too much data will damage her coding and cause her to go rampant.
Dr. Halsey also appears to have a far more ambitious view of Cortana's potential. She views Cortana as the solution to the perceived problem of Spartan independence; at present Spartans are carefully controlled through chemical pills they ingest to manage their emotions and thought-processes, but the Master Chief's encounter with a Forerunner artifact means these techniques are no longer working on him. Dr. Halsey foresaw this potential problem, however, and viewed the pills as only a temporary measure to control her Spartans. Cortana and her fellow smart AIs are her ultimate solution, binding the Spartans to her will. At this stage it's unclear whether Dr. Halsey imagines implanting Cortana in the Mjolnir armor, as in the main timeline, or whether she's actually imagining overlaying her AI consciousness over the Master Chief's own brain patterns.
There are clearly no ethical boundaries Dr. Halsey is unwilling to break, rationalizing her actions as necessary to ensure the survival of her race in the Human-Covenant War. In the case of flash cloning, her experiments are dangerously unethical and also highly illegal - flash cloning is typically viewed as a medical procedure, to create duplicate organs that won't be rejected by a body, but the flash cloning of full human beings is strictly prohibited and compared to the possession of illegal drugs. This is likely because a full flash clone retains consciousness, but has a very short life expectancy - and will inevitably suffer an agonizing, drawn-out and painful death. Some of the parents of Spartan recruits suspected the UNSC had kidnapped their children and replaced them; they were seen as conspiracy theorists, but this will only have reinforced ethical concerns over the technology.
Dr. Halsey used flash cloning to cover up the kidnapping of the Master Chief and his fellow Spartans. In the case of Cortana, though, she's using the technology in an unprecedented way - creating a duplicate of her own brain so she can fashion what she egotistically considers to be the next evolutionary step in the human mind. It will be interesting to see whether Cortana herself approves of Dr. Halsey's actions when she becomes fully conscious in Halo.