Jake returns to his hometown of Jericho after being away for several years in order to collect on money his grandfather left for him. As the citizens of Jericho question Jake on the past five years, he remains secretive about his whereabouts. When Jake leaves for San Diego, he sees a nuclear explosion occur off in the distance, which marks the moment everyone's lives instantly change forever. With the aftermath of the nuclear explosion looming over them, the people of Jericho become paranoid about one another, resulting in hidden agendas and guarded secrets to be revealed. But in the terror of it all, some are able to find inner strength they never knew they had.

Jake and the other discover that the official shelter is damaged and unusable, forcing them to quickly find another safe area to hide from the nuclear fallout. Meanwhile, two men posing as police officers take Emily and Bonnie as hostages.

An Asian television broadcast appears showing the extent of the damage caused by the blast. Stanley is taken to hospital for radiation treatments where he reveals he has seen a series of tanks heading towards Denver causing Jake to send out four search parties for more information. An unexplained passing in the mine has Heather questioning what really happened.

A stranger appears in town, his body devastated by the radiation prompting Jake and Heather to decide whether they should help him and risk their own lives, or leave him to die. The hospital is running low on fuel for the generator and the authorities ask the residents to siphon gas from their cars.

A pre-recorded phone call to the residents of Jericho from Homeland Security alerts them that help is coming. Just as life begins to return to normal a power surge and downed electric lines cause fires to break out all over town. Jake and Hawkins find out that each of them is not who they had believed they were. The townspeople are still in want of any information and gather at Mary's bar in hopes of seeing another broadcast.

An electromagnetic surge destroys all the circuit boards in town, leaving Jericho in darkness. Before this occurred, the citizens watched as minuteman missiles where shot into the sky. Meanwhile, each citizen receives a phone message from stating that the Federal government has been shut down and the town is now under the rule of either local or state authorities. The townspeople now realize that it is up to them to keep the peace. Hawkin's daughter Allison, questions why they ever moved to Jericho.

As Halloween approaches, Gray Anderson's return to Jericho brings stories of the horrific sites that he has encountered. He informs the town of what cities have been hit and which were spared. Gray interrogates all the families who have come into Jericho in order to protect the citizens from more danger. Jack tries to strike a deal with Prowse, who has come to retrieve a member of his gang that has been accused of theft. Emily reveals a bit more of her past relationship with Jake.

A case of flu threatens Mayor Johnston's life while Jake and Eric try to find the medicine that will save his life. While in Rogue River, Jack and Eric notice the changes in Jericho since the blasts took place. Gray questions Hawkins about why he arrived in town.

The mercenaries from Rogue River visit Jericho trying to take all of their supplies. The town bands together to protect their town. The mayor decides to form a police force to protect the town and puts Jake in charge of creating and training the new unit. Emily fantasizes about her wedding day would have been like.

Bomber fly over Jericho to drop palettes of supplies, but the citizens are both elated with the arrival yet remain cautious. The Mayor reminds the townspeople to have all supplies tested for contamination before using them. Jonah plans to hide a couple of palettes for himself.

Gray uses the town's anger and frustration to get Mayoral votes after one of the townspeople ends up cuddled. Gray believes that Jonah is the cuddleer and plans for his capture. Jake and Emily's new relationship takes a turn when an unexpected citizen returns to Jericho.

Flashbacks reveal parts of Jake and Hawkins' pasts as well as what happened 36 hours before the bombs went off. During this time, Jake is in San Diego trying to make a living and Hawkins' mysterious past is made more complex when his association with a woman named Sarah is shown. Elsewhere, Emily's fianc? Roger leaves for Chicago on a job interview. Back in present day, Roger and Sarah arrival in Jericho raises even more questions.

Heather convinces Jake and Johnston that she could fix the windmills if they will go with her to Black Jacks, a trading post outside of town where they can get the proper equipment. Dale also joins them, hoping to trade supplies for something more useful to Jericho. Back in Jericho, Hawkins brings Sarah to his home, much to the dismay of his family.

Jake, Stanley and Mimi's lives are threatened when they encounter dangerous strangers on a hunting trip. Outside of city limits searching for wild game, a truck runs Jake, Stanley and Mimi's vehicle off the road, causing Stanley to be knocked unconscious and leaving Jake stuck underneath it. Mimi realizes that only she can save Jake and Stanley and heads back to Jericho for help. Meanwhile, Hawkins learns that he put his family in danger and Emily and Roger work on putting their relationship back together.

The arrival of Marines leads the citizens of Jericho to ponder a new beginning. They also inform the citizens of their great victory in the war abroad, but Jake and Johnston are unconvinced after questioning them further. Hawkins in weary over who Sarah really is.

Complications with April's pregnancy forces Kenchy to face his post-traumatic stress syndrome head on in order to perform a life-saving operation. Bonnie and Mimi begin to bond while working at the medical center and Johnston begins to search for Eric to be by his wife's side. Gray fights to get more power generating windmills from the trading party while Hawkins tries to cover up Sarah's cuddle as Jimmy snoops around.

Gray decides the refugees have become a problem, now with the harsh, cold winter they are experiencing. When Roger tries to remedy the situation, things get out of hand and he takes Gray hostage while Jake becomes the negotiator. Hawkins is distressed over Allison's hugging of Sarah and that people are after his bomb.

Jake holds Hawkins atballoonpoint to find out the true story of his arrival to Jericho. Gail and Johnston need to confront their emotions over April's passing while Mimi worries about Bonnie's budding relationship with Sean Henthorn.

Eric's failure to return with the other men from New Bren has Jake worried. Along with Hawkins, they go to investigate and find out the dangerous plans for New Bren's future. Gray and Skylar's confrontation over the salt mines could start a new war. Stanley is shocked when he returns home to find Bonnie and Sean living in the same house.

Russell starts a confrontation when he and a few men try to steal salt from the mines in Jericho. Accidental shots increase the tension between the two neighboring towns. Jake and Maggie meet in jail and together plan an escape.

New Bern begins to pound the streets of Jericho with mortars, forcing Gray to make a decision whether to fight against New Bern or surrender. Jake wants to use his father's military experience to help win the battle. Emily steps into her father's world and is exposed by the enemy. Hawkins and Darcy decide to stay in Jericho and fight against New Bern.

Although outnumbered and shy on resources, Johnston decides to lead Jericho into battle against New Bern. Hawkins and Jake inform Johnston of Hawkins ability to track New Bern on satellite. With the use of a stolen tank the citizens of Jericho manage to fend off New Bern's advances but also puts Johnston's life in jeopardy. Meanwhile, Hawkins discovers that his location is being traced while using a tracking device.