First season
The storyline centers on the residents of Jericho, a small northwest Kansas town, in the aftermath of a nuclear attack on twenty-three American cities in the contiguous United States. The series begins with the sighting of a mushroom cloud of unknown origin over Denver, Colorado. Initially, it is assumed to be an accident, until a teenager reveals a recording of a phone call from his mother in Atlanta, Georgia, which is cut off by the sound of an explosion – demonstrating that the Denver disaster was not isolated, and thus unlikely to be accidental.
Problems are compounded by loss of power and modern communications, effectively isolating Jericho. Later, power is restored to Jericho by what is alluded to the efforts of the U.S. government but an electromagnetic pulse (EMP) from an unknown source disables all electronics.
While the first few episodes center on restoring life, following the attacks, about halfway through the season some citizens of Jericho meet with citizens of a nearby town, New Bern. At first, relations are established, resulting in a trade of windmills (for power), built in New Bern's factory, for supplies for food from Jericho's farms and salt from its mine (neither of which New Bern could supply on its own). Relations begin to sour as New Bern puts the blame on Jericho for its problems and the New Bern sheriff eventually declares war, leading to the season's climax.
Themes regularly addressed in the show include the gathering of information, community identity, public order, limited resources, the value of family, hardships of fatherhood and internal and external threats. The show also features several mysteries involving the backgrounds of major characters, the perpetrators of the attack and the extent of damage to the United States and its government.
The pivotal character in the story is Jake Green, the 32-year-old son of Mayor Johnston Green. Jake had fled the town of Jericho five years earlier, after he became mixed up with the wrong people and was involved in questionable activity. He briefly returns home to claim his inheritance, before being stranded by the catastrophe. After a somewhat awkward return home and a tense reunion with his father, Jake steps up to become a leader in Jericho, fighting to protect the town and its citizens. As the people of Jericho struggle to survive in a changed world, most remain unaware that one of the newest residents, Robert Hawkins, knows a lot more about the attacks than he is letting on. It is later revealed that he is in possession of an unexploded nuclear bomb, intended for the attack, but how he obtained it and his allegiance remain unclear.
Gray Anderson encounters a Federal Emergency Management Agency (FEMA) camp outside of Topeka, where he learns that the attack on New York City was foiled by alert New York City Police who arrested the bombers before they could detonate the 20-kiloton nuclear bomb in the back of a van. Anderson also reports that Washington, D.C. has been bombed. On the way back from the FEMA camp, Anderson's car is stolen by looters and he is forced to walk home to Jericho. Anderson also discovered that Lawrence, Kansas, was targeted, and that the governor is missing. Robert Hawkins receives a Morse code message on a ham radio stating that Denver, Atlanta, Chicago, Philadelphia, Kansas City, San Diego and several more cities (not shown) have been destroyed. A black box flight data recorder that Jake recovers from a crashed airliner indicates that air traffic control is non-existent, a mushroom cloud was seen rising 16 km (9.9 mi) into the atmosphere and that flashes had also been seen towards Texas.
A radiation-burn victim walks into Jericho from Denver, leading a rescue party to Bear Lake, but the 20 radiation-burn victims there are dead. Before the unnamed radiation-burn victim dies, while he is interrogated by Hawkins, it is revealed that he is an accomplice of Hawkins and that there is a traitor in his past.
In the first season finale, armed residents of New Bern attack Jericho with crude mortars made at the factories in New Bern. The mortar bombardment injure people in Jericho. Jake and Johnston Green along with Robert Hawkins lead a counter-attack on New Bern's forces outside of town, killing many of the attackers; Johnston Green is fatally wounded. Army units arrive to separate the combatants just as the season ends.