Three years into the zombie apocalypse, a ragtag team of everyday heroes comes together to transport the only known survivor of the zombie virus from Upstate New York to a lab in California, in hopes of using his blood for a vaccine. A zombie baby proves to be an early obstacle, and what they don't know is that their last, best hope for a vaccine is hiding a dark secret that threatens them all.
In the season 3 premiere, Warren and gang are taken prisoner, while Murphy escapes the sub with his newly formed group of blends, Dr. Merch, and 10K. Sun Mei arrives with a commando team capturing the team, Doc, Warren, Addy & Hector and moves to collect a supply drop but run into the “Enders” - psychotic humans. The supplies are stolen by Murphy and his blended team including 10K.
On the road to find Lucy in Illinois, Doc and Addy are forced off the road by a retro presidential limo. Turns out Sketchy is running for "President of the Apocalypse" with Skeezy as his campaign manager. Doc and Addy follow them to Wall Drug, South Dakota and witness the somehow lucrative, always entertaining train wreck that is Sketchy and Skeezy.
Warren's Apocalyptic Dream of a Black Rainbow sends our heroes on a mysterious new mission to save the Apocalypse from something even worse. Warren awakens from a Coma to find herself in ZONA two years later, with Murphy seemingly cured, and the rest of our heroes either dead or fighting for their lives against unkillable "MAD-Z's" caused by an evolving Zombie Virus.
Driven by her dream of a black rainbow and flesh eating rain, Warren and Murphy escape Zona; Doc, 10K and Sarge are pinned down by snipers.
By the time Warren and the others make it to the refugee camp, Red and Sun Mei have mysteriously vanished along with everyone else. After convincing 10K to give up the search for Red, Murphy and the others decide to head to Newmerica with Sarge – but Warren has her own plan. Driven by her dream, Warren is compelled to head east instead of north.
Following Warren's dream, the team doesn't stop while crossing The Great Pile, a seemingly endless landscape of rubble and destruction.
The team is captured by an Unseen Force and enslaved in an elaborate underground facility, forced by their mysterious captors to perform a series of bizarre, dangerous tasks.
Lucy fights to save Murphy's life; Warren and the others battle a biologically modified Franken-Zombie guarding a clue to Warren's dream.
Shaken by the death of one of the team, something snaps in Murphy, and Warren is unable to stop him and the others from committing an atrocity as misplaced revenge.
Warren and the others encounter a mysterious stranger who they think is a grave robber but is something much more.
Back at the dawn of the apocalypse, newly promoted news anchor Carly McFadden struggles with office politics and office zombies as unsettling reports start to come through to the news desk. Eight years later, the group explores the abandoned TV station as they look for a way to contact Kaya at camp Northern Light as she attempts to hide from an invasion of ZONA forces. Fearing the worst when her hideout is breached, she takes a last stand, only to find that Citizen Z has returned home after two years.
In Chicago, Doc and Murphy encounter Sketchy, Skeezy and others at a barbershop, though the others continually attempt to betray them.
The group returns to Mercy Labs, where they first encountered The Man, to retrieve another item that Warren's dreams show her.
The group arrives at Mount Weather to find the remains of the government and learns they need the thumbprint of the President of the United States to achieve Warren's goal. They meet the remains of the government and learn more about what Warren's dreams are, and that the government has plans that differ from their own.
The team arrives in Washington D.C., and goes to finish Warren's goal. This causes Warren to realize why her dreams are happening, and that she was trained to activate the Black Rainbow, not stop it. When she attempts to stop it, a scientist from Zona interferes. She is sent off in a jet as it activates, and Murphy is struck by flesh-eating bacteria while trying to save her. As the Black Rainbow becomes a reality, 10K and Lilly start a relationship, while Doc and Murphy silently watch what they believe to be the end of the world.