Doctor Leonard Church, also known as "The Director" by most of the characters, is a horrorcow, who builds an entire military organisation and does horrible things to his employees and his daughter in an attempt to bring his dead wife back and make her invincible.
This guy starts out trying to get into the UNSC military. At the academy, he meets a girl named Allison, who saves his ass from some jock-types. The two of them eventually develop a relationship, but Leonard washes out, while Allison graduates. Leonard goes on to get his doctorate in... something, probably AI Theory considering the nature of his later experiments.
Well, then Allison goes and dies in the Covenant war. Doctor Church decides to try and make the military better, and creates Project Freelancer, which involves pairing human soldiers with AI units to increase their combat capabilities. However, he is only given permission for one AI... so he cheats.
He creates the AI based on himself, and dubs it Alpha. He decides that, since this AI is technically him, he can fragment it into smaller chunks of AI. He does this by psychologically torturing Alpha until it can no longer remain sane, and breaks off a piece of itself to stop it feeling the emotion that is being targeted. In doing so, he shatters Alpha's mind so severely that he loses his rage (Omega), logic (Delta), creativity (Sigma), deceit (Gamma), trust (Theta), happiness (Iota), fear (Eta) and memory (Epsilon). By the end of it, Alpha, a sentient being, is completely non-functional, doesn't remember who he is.
Things aren't even this bad, however. When Alpha was born, he immediately severed his memories of Allison, becoming another AI called Beta, who happened to be a perfect recreation of Allison. Leonard implanted Allison in a superhuman robot body, determined to ensure that she could never die again. However, he also manipulated her memories, since Beta had no idea that she was a robot, and no idea that Allison and Leonard had a child. She became Agent Texas of Project Freelancer, and was given all the best equipment and tasks.
Then he starts a fake war to train his soldiers. He doesn't use VR or regular training exercises, he creates a phony Red vs. Blue war in order to create live fire simulations for his agents to train in. The two armies are composed entirely of academy washouts, mentally handicapped soldiers, and PTSD-afflicted veterans.
Then there's how he treated his daughter. Her birth name is unknown, but, in order to get her father to notice her, she joined Project Freelancer and became Agent Carolina. Carolina trained herself to be the absolute best of the Freelancers, and was rather smug about it. He did seem to show her a little favouritism, granting her two armour enhancements, but that was really about it. He also kept firing MAC Cannons at her boyfriend, Agent York, though that was probably more coincidental. She was then pitted against Tex, technically her own mother, which fueled an envious hatred, and led to her demanding two AI units when she discovered that Tex had Omega, supposedly the most powerful of the bunch. This was extremely dangerous and almost caused Carolina's mind to tear itself apart, but the Director decided to let her do it anyway.
Leonard used his soldiers like guineapigs. Obviously, sticking PTSD-corrupted AI shards in their heads was rather dangerous. However, he then there's the case of the Dakota twins. Agents North and South Dakota were twins who were grouped together constantly. He gave them the same armour colours, assigned them to work together on missions, and constantly made them compete for the top spot against each other. He then gave North an AI and didn't give South one, fueling a jealousy that eventually led to South betraying North and leaving him to be killed by the Meta.
When Epsilon was harvested from Alpha, the Director took this insane lump of severed memories and decided to implant it in one of his soldiers anyway. For science. Epsilon was loaded into Agent Washington, and immediately committed suicide the moment it came online, driving Wash half-insane himself.
Tex discovered what he was up to and brought much of the project crashing down, but the fight left Carolina injured and resulted in the Meta throwing her off a cliff. Leonard barely gave a shit and focused his efforts on finding the now-renegade Tex instead.
He then began a frankly ridiculous amount of damage control. He sent Alpha to a remote facility where nobody could ever find him, and sent Agent Florida to guard him. Instead of saying that Florida died during Tex's rampage, he decided to deny that there ever was an Agent Florida, on account of there not being a Florida anymore. He then had the entire state broken up and sunk into the Atlantic!
He then found a random Blue team soldier and had Alpha implanted into his body, completely overwriting his personality and allowing them to tell Alpha that he was a human soldier named Private Leonard L. Church.
Project Freelancer would collapse, but the Director escaped justice because of the protagonists' stupidity. However, he also found out during this time that Tex wasn't invincible. Her body had been destroyed more than once after she met up with Alpha again, and she eventually got absorbed into the Meta, a group of AI possessing Agent Maine. She would then be killed alongside all of the other AI except Epsilon when an EMP was set off. He discovered that his obsession with her had become tainted by her death, to the point that it was all he really thought about. So when Alpha splintered off his copy of her, she became the Failure AI, and no matter how hard she tried, her goal would always be torn away from her just when it was within her reach.
So how did Doctor Church decide to solve this? By creating another Beta AI and fragmenting her! He was determined to break off the part of her that made her fail, and so tortured his own wife until her mind literally shattered into a hundred pieces. He implanted each of these into a robot body and used them to fight Carolina, who had survived her fall because she had a grapple gun.
When Carolina and AI Church broke into his office, they found him constantly watching a video he recorded of Allison before she left for the war. Even after everything, he only referred to his daughter as "Agent Carolina". He then had all of the systems, including life support, shut off, and sealed himself in his room with the video, before shooting himself in the head.
