Jacob was in a relationship with Catherine Halsey and they had a child together, Miranda Keyes. Their romantic relationship ended and Miranda grew up with her father. As such, Miranda had an estranged relationship with her mother despite Jacob's best efforts to humanize Catherine in Miranda's eyes.
Master Chief Goes AWOL
Captain Keyes visits his daughter Dr. Miranda Keyes in her lab. He informs her that the Madrigal survivor she spoke with succumbed to her injuries. This confuses Miranda, who didn't see any visible injures on the girl. She realizes that an Article 72 has been ordered. The UNSC's willingness to kill an innocent child disgusts her. Captain Keyes tries to remind her that sacrifices have to be made to save humanity, and her willingness to lie about the Spartans jeopardizes their mission. She can't see the point in saving humanity if they're going to lose their own in the process.
Meanwhile Master Chief John-117 goes AWOL after breaking UNSC protocol by refusing to kill the Madrigal survivor. He disables the ships surveillance systems, causing a mass panic amongst the UNSC. Captain Keyes and Admiral Parangosky try to quell the masses, but speak with Halsey who admits she thinks John is having memories, which Keyes knows shouldn't be possible. Master Chief's ship is manually overridden and lands in the landing bay, with marines ready to shoot him down. A blast of energy knocks out the power in FLEETCOM, allowing Master Chief to escape while everyone watches in surprise.
The committee calls an emergency meeting to discuss Master Chief's status. Other members in attendance include Admiral Margaret Parangosky, Fleet Admiral Hood, and Keyes's ex-wife Dr. Catherine Halsey. Hood isn't sure punishment for Master Chief is fit since he's a symbol of hope, a heroic statement, and a punishment would be bad for morale. Halsey undermines Admiral Parangosky by pitching the Cortana system to the council. She explains that it will overwrite Spartan consciousness and replace it with an artificial general intelligence. She believes it to be the next state in human evolution. The Spartans were the first step, while Cortana is the upgrade. Cortana represents the sum total of every available date point, holding the intelligence of the galaxy in her mind. She hopes to use Cortana to create Spartans who are more lethal, their judgement error-free, their performance upgradeable, and controllable. Captain Keyes reasons that Spartans such as John are people, but Halsey disagrees as he's much more than that. She thinks the Cortana system can help them win the war against the Covenant. Jenma points out that Halsey's previous theories depended on biological substrates derived from the illegal practice of human cloning. Halsey, however, has found a way around that. Parangosky reluctantly authorizes a trial of the Cortana system.
Master Chief turns on his beacon and allows his arrest by the Spartans. He is taken through FLEETCOM by Captain Keyes and others, where he watches Halsey drive off with the Covenant artifact. A UNSC Gladius ship was hijacked by the Covenant and all inside were annihilated. Miranda tries to decrypt the Covenant broadcast from the hijacked UNSC ship, assuring Captain Keyes that she'll look into translating it more. He tells Miranda that Halsey is about leave for a mission, and if she wants to examine the artifact, she has finally has an opening. Hasley, Master Chief, and her assistant Adun find the larger keystone on the planet Eridanus II. Subsequently, Captain Keyes, the Spartans, Miranda, and other UNSC members are called to Eridanus-II.
Truth About the Spartan Program
Captain Keyes has a history on the planet, as he previously visited the planet with a pregnant Halsey when John was a child. Master Chief confides in Keyes about his memories of Halsey visiting him as a child. He came to Keyes first to learn the truth as the man has always been there for him. This is something that Keyes promises to look into personally. However, Keyes tells Halsey and Parangosky about the revelations. Parangosky wants to cease all the operations including the Spartan protocols by bringing everyone back to Reach immediately with the artifact. She wants to terminate Master Chief. Halsey admits they could but leverages the fact Parangosky knew the true origins of the Spartan program. She kept all the files and will release them if Parangosky doesn't keep the program going. The woman concedes angrily. Keyes wants Miranda removed from the artifact studies to keep her hands clean. Halsey quips this is the only parenting issue they can agree on.
On another ship, Miranda marvels at the technology of the keystone and what it could mean. Jacob joins her as she revels in the ideas of what to do next with the artifacts. Jacob tells her that she's been removed from the artifact studies effective immediately, which deeply upsets her. He clarifies that it's an order so she leaves him. Later in the day, the Covenant breach slipspace to attack the UNSC. A viscous fight ensues, with Halsey demanding that the Spartans get the artifact to her. Keyes drives a Warthog that the Spartans tail on-foot as the try to get the artifact to safety. They struggle to reach her ship so she redirects them to Miranda's ship, which explodes in fire, forcing her to redirect them to herself again despite the dangers. Keyes surrenders the Warthog to the Spartans to assist the marines, who are being overpowered by Covenant forces. Master Chief witnesses Kai in danger with the marines and diverts from the plan despite Halsey's screaming orders to keep with the plan. Master Chief tries to fight the brute but it knocks him across the field. The artifact is ultimately stolen by the Covenant.
On the flight returning to Reach, Keyes informs John they couldn't track the departing Covenant ship; John blames himself for losing the artifact, but Keyes reminds him that he saved one hundred and fifty lives - including his. He's a hero, though John doesn't feel like one. When the arrive at Reach, Keyes assures John they will regroup and come up with another plan. Once inside, Keyes meets with Paragonsky and three other members of the security council about the failures on Eridanus. The security council mentions that Admiral Hood is considering dismantling Section 3 to put the Spartans directly under the control of the UNSC. Parangosky is quick to assume the source of those ideas. Later, John tells the UNSC of Makee's revelation that the Covenant's holy planet is located in the Aspero star system, and is called Raas Kkhotskha. Keyes leaps into action to find the planet in the otherwise barren system.
Halsey is questioned by a representative from the Judge Advocate General. Parangosky and Keyes watch in secret, with her admitting to Keyes that she's made Halsey the scapegoat for the entire operation. He doesn't think this is a good idea but she shushes him, as the general has been instructed to limit his questions to cloning. John interrupts the meeting and makes the general leave, at the same moment that Miranda materializes in the room. Keyes is upset as Miranda doesn't have clearance, but Parangosky keeps him quiet. They listen to John and Halsey's conversation.
John asks why she did it. Nothing she says will make sense until the benefits manifest. She's accepted that he will hate her. She was planning the future of their species since natural evolution is failing them since humans are still hardwired for conflict and selfishness. If they were going to survive they needed a force that would intervene and prevent conflict before it started. She created the Spartans to protect humanity from itself. He wants to skip to the part where she kidnapped them. She needed children, no older than six, so their training and augmentation could be carried out properly. They were too young to volunteer and parents don't give up their children very easily. The thing she replaced him with was a genetically compromised clone that began exhibiting signs of illness before passing away. It allowed the parents to properly grieve the loss of their child and give them closure. She views this as a reasonable, a statement he throws back at her. She lied to them for years while they fought and killed for her. She corrects that it wasn't for her.
Any challenge to the status quo is always thought to be mad until people see the benefits. He asks who knew about the truth so she covers up for her partners by saying everyone looked the other way. She thinks it was worth it to unlock the mystery's of the artifact. They have upended everything she thought she knew about their place in the universe. He's the key to unlocking more secrets. He has a confection to the thing they're calling the Halo. She knows he will take them there to lead their species beyond its current limitations. He needs her to do it and ensure their sacrifices aren't in vain. He plans to finish what they started without her. Miranda disconnects from the link, not giving Keyes a chance to explain himself or his knowledge of the programs origins.
Parangosky checks-in with Keyes later in the day for an update on locating the Aspero star system. He reveals there's a reason the star system isn't explored - there's nothing there. Parangosky and Keyes watch John with Makee. She worries about John's growing connection the human girl Makee, as he's not acting like a soldier while frolicking in the garden with her. She also worries that he knows of her and Keyes' involvement in the program, since Halsey answers to her. Keyes disagrees that he knows, and in the meantime, they have to trust John - he's a still a solider who's always on mission.
The planet Agade is glassed by the Covenant, killing three-million innocent people. Keyes watches the panicked video message from the governor of the planet before it was glassed. John returns to FLEETCOM where he talks with Captain Keyes, as everyone is devastated by the loss. Master Chief thinks Makee can make contact with the keystone to find the Covenant planet, though Keyes and Parangosky are skeptical. Chief reminds them that he overcame decades of indoctrination, so she can too. He trusts Makee, a sentiment that holds weight for everyone.
Miranda turns her focus back to the Gladius recording. Jacob visits her and expresses an interest in her work, so she explains that the Covenant voice is different than others she's heard before. It has an accent or impediment that she can't quite isolate yet as the frequencies are improperly balanced. He's sure that she will figure it out.
Jacob visits Halsey to say goodbye before she departs, as Parangosky wants her off the planet by noon. That's the same time as the artifact test, so Halsey tries to delay her departure, but Keyes reminds her that she's a liability. Halsey snaps back that he shouldn't play the good guy - he's supposed to have her back. She doesn't have time for his self-righteous anger. Keyes is angry at her, himself, and system that so easily sacrifices human life in the name of progress. He's also that her obsession with the program has cost her every relationship she has. Asking her what else she’s willing to sacrifice, Halsey admits she's willing to sacrifice everything. Taking Halsey's hand, Keyes admits that he pulled some strings to let her ship, which is fueled and waiting on the tarmac. She has to leave by noon.
Miranda continues to work on the transmission throughout the day, and when the transmissions become clearer, she is both horrified and surprised at the discovery of Makee's voice. She tries to call Jacob but learns that systems are down, which she immediately equates to being Halsey's doing. Parangosky, Jacob, Makee, and an MP are in the secure testing room, waiting for John and Makee. Parangosky tells the MP to find Makee and John. The MP returns with who tries to explain that John is in danger as the Spartans have turned on him, but Parangosky laughs at the ridiculous claim. Makee sees the artifact and speaks Shangheili. She explains that she escaped as John spoke with someone in his head, who Keyes notes as being Cortana. She was sent away but John stayed. Miranda rushes in shouting for them to keep Makee away from the artifact as it was Makee's voice on the Gladius recording. Makee tries to explain that she had no choice but an MP grabs her. As she struggles, he uses an electric rod to shock her. Makee calls out to the keystone in Shangheili, jarring the guards enough to where she can break free of their grasp. She steps forward and touches the keystone, making it emit an energy blast that knocks everyone in FLEETCOM to the ground and disrupting all the technology in the vicinity.
Master Chief rushes into the room a few minutes later to find a guard burnt by Makee's activation of the artifact. Miranda tells Master Chief that Makee escaped with the artifact. He hurries out of the room but is blocked in the hall by Riz and Vannak. Riz has a gun to Kai's head while Vannak points his at John's. Miranda and Jacob arrive in the midst of the conversation, but hear John trying to reason with the Spartans by telling them the truth of Halsey's horrendous actions. They don't believe him until Jacob admits to being privy to the activities and helping to plan their kidnappings, replace their bodies with clones, and erase their memories. If they want to shoot anyone, it should be him. John adds that if they lose the artifact, they lose the war, and the Spartans are the last chance for humanity. Miranda silently listens to the revelations. The Spartans each make a plan and rush off, leaving Jacob to attempt an explanation to Miranda, who walks off without any interest in speaking to him.
Jacob orders the UNSC track for Halsey's now-escaped ship, later tracking her escape pod when the actual ship crashes. Once John suits up, Keyes reveals that Halsey's ship has been found in Manasses. He expresses regret for the things he's done to them. He rationalizes it by looking at the good the Spartans have done, but knows it doesn't change anything. John knows there will be a reckoning someday, but not today. Keyes leaves the ship as the rest of the Spartans prepare to leave. After Halsey is captured by soldiers, Keyes tries again to talk with Miranda, but she ignores him. He watches from an adjacent room as the captured Halsey goes into a seizure that Melinda recognizes as being a clone, as the real Halsey is still out there. Keyes places Halsey's photo on the top of the UNSC's most wanted list.
Captain Jacob Keyes is described a dedicated military man, a war hero and a caring father. He finds that working alongside his daughter and his ex-wife is usually the cause of conflict rather than comfort.
Behind the scenes
He is based on the character of the same name, Jacob Keyes, from the video game series.
- Halo: The Television Series - Season One, Contact
- Halo: The Television Series - Season One, Unbound
- Halo: The Television Series - Season One, Emergence
- Halo: The Television Series - Season One, Homecoming
- Halo: The Television Series - Season One, Reckoning
- Halo: The Television Series - Season One, Solace
- Halo: The Television Series - Season One, Allegiance
- Halo: The Television Series - Season One, Transcendence