Protocol Omega means the Director is no longer intervening in this timeline as either the Traveler program succeeded in its mission or it has totally failed. When Jeff visits Marcy to offer his condolences, she realizes he has been overwritten by 001 and eventually kills herself to prevent him obtaining Ellis' backdoor code from her brain. 001 uploades his consciousness to the internet, enabling him to exist into the future and ultimately gain control. He sends the consciousnesses of his followers into world leaders, provoking the Russians and Chinese to launch nuclear warheads against the US. Yates blames MacLaren and his team for hastening, rather than preventing, the end of mankind. MacLaren uses 001’s machine to send his mind back to the August 2001 day when his host first met Kat. He tells her to give John a second chance, later drops off a warning about Helios, then on September 11 arrives at the same office high in the World Trade Center a few minutes before 001's expected arrival, meant to kick off the Traveler program. MacLaren sends an email, knowing the Director will find it, stating: "Traveler program failed. Do not send 001." MacLaren stays in the office – as 001 was supposed to do in the original plan – to await the attacks. The non-Traveler Marcy, showing no signs of hydrocephalus and working as a nurse, happens to sit beside David on a bus, and he strikes up a conversation, renewing their inevitable connection for a third time. The Director decides that Traveler program version one has failed, and begins version two...
To prevent an explosion that kills thousands, the team steals antimatter from a military convoy. The material's intended recipient is a new traveler who fails to prevent his host's suicide, forcing the team to improvise. After failing to upgrade their containment device, the team returns the antimatter to its origin facility. They form a tenuous alliance with Dr. Delaney, who produced the antimatter; history records her as complicit in the weaponization of antimatter, but she actually opposes Major Gleason's ambitions. MacLaren informs Delaney that they will return soon. Philip retains his host's heroin addiction. MacLaren meets his wife, Kat, but also resumes a preexisting relationship with Carly. Marcy works to build trust with a confused David.
It's not a special-effects-heavy show. Instead, it focuses on squeezing every drop of juice out of the slightly off-kilter premise. For a start, "taking over" present-day human hosts kills them. So there's a massive built-in moral dilemma. And it's worked out with painstaking logic. Time travelers try to pick people who were about to die anyway - but this too presents problems. The time travelers need to remain undiscovered, which means seamlessly picking up the threads of their hosts' lives. Time travelers may have motivations of their own, which need to be dealt with in the present. It all meshes beautifully.
During an update for historians, one of them dies from cerebral overload and is taken over by another traveler. The faction then breaks in and kidnaps the historians. A Blackbox is a device used to extract information from an unconscious or dying person and the team uses one to access a critically injured Hall to ascertain the location of historians. Jeff reaches out to his police sergeant to get his job back and is told to get help from a social worker first. Philip is questioned by the faction. Philip is given time with Kyle as a gesture of good will, who states that he sympathizes with the faction's goal, especially since he just saw another historian die during the update. Faction saves a TELL that Kyle provided to gain his support. Jeff reaches out to David to sign his therapy form for him to get his job back. David agrees to help as a social worker with Jeff's addiction, which the traveler doesn't actually have. Hall is able to relay information from when he was tracking his team's historian showing he ran into a faction team and was shot climbing a fence. He reveals that it was Kyle and Luca from his own team that shot him. Hall is able to show the team the location of the historians and the team is dispatched. While with David, Jeff receives a message to meet up at the location for tactical support. Philip is able to escape before being cornered by Kyle and Luca. Maclaren's team shows up just in time to save Philip and kills Luca and Kyle. The team saves all the historians while taking out many of the faction. Hall is told he saved them all and is able to pass away in peace knowing that. Jeff and Carly reconnect. Philip is seen throwing out his yellow pills that historians have to take.