Nash and Joe are tied up in the back of a cigarette boat speeding along in the Bay. Drug dealer Mario Torres has found them out, and are leaving Nash and Joe for dead. Torres and his bodyguard jump from the boat into another boat. As the abandoned boat is about to crash into a freighter, Nash frees himself and Joe, swerving the boat out of harm's way. Nash and Joe return to Torres' dockside drug factory and arrest Torres.
Meanwhile, the dead body of police officer Frank McNally has been found. McNally has been shot, stabbed and strangled. A cell phone on the body rings for Nash. The caller informs Nash that a bomb is hidden somewhere in the City, and that the bomb is set to go off at 4PM tomorrow. To find the location of the bomb, Nash must kill Joe Dominguez, his partner.
Another call from the bomber is visually tracked by Nash with binoculars. The bomber narrowly escapes, leaving behind his car. Inside the car are timers, detonation cord, and other bomb making materials. The SIU goes in search of Jimmy Bangs, a dealer in explosives.
The bomber's car actually belongs to a SFPD Bomb Squad member. Joe, Harvey, and Officer Ronnie raid the member's house, only to find him dead, hanged from his ceiling fan. Police rookie Cassidy, now in uniform, is assigned to the SIU. Meanwhile, Antwon Babcock joins the SIU, taking Evan's desk. On surveillance, Antwon catches Jimmy Bangs. On interrogation, Jimmy reveals nothing.
The cell phone is traced to an abandoned building. Nash remembers the building as the hiding place for young Angela Pritchard, who was kidnapped by Edward Strode. An old newspaper left on the table describes the crime, as Strode calls Nash again. Strode informs Nash that his deadline for setting off the bomb has been moved up six hours. Strode still wants Joe dead, to get even with Nash for killing Strode's wife during the rescue of Angela Pritchard.
According to prison records, Strode was diagnosed with terminal cancer and died four months ago. But records were faked and that is how Strode escaped prison. Cassidy discovers in police records of the Angela Pritchard kidnapping that evidence photos are altered, meaning that investigators Frank McNally and Vera Peralta were in on the crime by covering up Strode's identity.
Antwon finds Jimmy Bangs money stash, with fresh bills sequentially minted in 1994, the year of the kidnapping. Jimmy finally agrees to talk - Jimmy sold Strode 100 pounds of C4 explosives. Jimmy is to meet Strode at the Ferry Plaza at 4PM. Nash shows up instead, and Strode is there, his hand holding a dead man's switch. After a game of chess, Strode manages to escape by setting off a diversionary bomb hidden in a trash can.
Antwon and Harvey raid Strode's former cell mate's place of business, and this is also where Strode has been hiding out. The cell mate informs them that Strode bribed the San Quentin Medical Examiner to issue a fake death certificate for Strode, and that Strode escaped prison by posing as a dead body.
Joe and Cassidy go to arrest Vera Peralta - she has just returned from vacation. But Strode is there also, taking Joe and Cassidy hostage. Strode calls Nash, giving him a choice of which one to save - Joe and Cassidy are in different locations with bombs strapped to them. Nash is forced to choose Cassidy, but Antwon is told to locate Joe with clues from the background (gang signs painted on a garage door signaling their turf, which indicate location). Vera Peralta is found shot dead.
Cassidy is on Alcatraz Island. Nash takes the cigarette boat to the island. Nash frees Cassidy and disarms the bomb. Strode confronts Nash, but Nash shoots Strode dead. Joe is found with no bomb, and the bomb with Cassidy is a fake. The real bomb is in the trunk of McNally's car, parked in the SIU parking lot. Antwon drives the car into the Bay, where it safely explodes in the water.
Joe and Inger have been forced to move out of Nash's building, so that Cassidy can have a place to live. Joe and Inger find an expensive house that the owner is underselling for half price. But as Joe and Inger take possession of the house, Inger falls through the floor as she sits in the bathtub. Nash's father Nick has increasing symptoms of Alzheimer's, as he sets a place for Nash's brother Bobby. Nick thinks that Bobby is coming home for dinner.
For more, see commentary for Episode 101