The Faction sets off nuclear blasts that destroy all of the Travelers' archives outside the US. David, left for dead by the Faction in the last surviving archive, is the only person who can disarm the nuclear device. He succeeds but is exposed to lethal radiation. Kat's suspicions about MacLaren, temporarily allayed, surge again and she throws him out – for her the marriage is over as she feels he is no longer the man she first met. Jeff tries to escape from interrogation by 001; he is eventually found having been walled up. Marcy hopes the Director will send a Traveler medical team to save David but no help arrives. In the moment before he dies, David conveys a message from the Director: "Protocol Omega."
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.
The Director can invoke three other protocols in special situations: Protocol Alpha temporarily suspends all other protocols when a critical mission must be completed at all costs, Protocol Epsilon can be invoked when Traveler archives are threatened, and Protocol Omega permanently suspends all other protocols when the Director abandons the Travelers because the future has either been fixed or deemed impossible to fix.
In 2004, the St. Paul and Travelers Companies merged and renamed itself St. Paul Travelers, with the headquarters set in St. Paul, Minnesota. In August of that year, it was charged of misleading statements associated with the merger. Despite many assurances from CEO Jay Fishman that the newly formed company would retain the St. Paul name, the corporate name only lasted until 2007, when the company repurchased the rights to the famous red umbrella logo from Citigroup and readopted it as its main corporate symbol, while also changing the corporate name to The Travelers Companies.