Season 3 picks up ten days later at the funeral of a fallen cop. Paul meets with Sid at the gravesite, but fails to get a confession. The fallen cop is Archie Garrett, Sid's partner.
The team has been tracking Sid for two weeks, but he hasn't confessed to his deal with the Solanos, the cartel bloodbath or Mike's murder. Sid is targeting the Graceland team, but they don't know who's next.
The house is a mess and Dale wants the team to clean up, but Johnny refuses.
Paige is Sid's next target. While driving in her truck, a motorcyclist attempts to gun her down. Paige swerves into the hit man and crashes both the motorcycle and her truck.
Mike, alive and well, gets an MRI. As Briggs wheels Mike back to his hospital room he explains Sid must believe he's dead.
Mike asks how Paige is doing after Sid's attempted hit. Briggs reassures Mike she's fine, but wants to tell the team and the bureau that Paige betrayed Mike. Mike refuses. He makes Briggs promise not to tell anyone.
Mike thanks Briggs for saving his life, but Briggs deflects saying it was the nurses and defibrillators that saved him. Briggs flips through Mike's journal and it's filled with strange numbers and sketches. He asks Mike about his near death experience, but Mike deflects with a joke. He's hit with a sudden pain attack. Briggs encourages him to fight through it, but Mike medicates instead.
Special Agent In Charge Shawn Logan summons Briggs. He has the tape of Juan Badillo's murder, found in Mike's belongings. Logan informs Briggs he can either help take down an Armenian mob or be indicted for Badillo's murder. Briggs agrees to go undercover.
Paige confronts Sid at his home. There's an inquest and she wants to get their stories straight. Sid strangles Paige and threatens to kill her, but ultimately agrees to a meeting.
Tevan Adamain is second in command for The Sarkissian Family- an upper echelon arms dealers. Tevan is in kidney failure. Given his failing health, his nephew Ari Adamain is in line to be second in command.
Ari is trying to get a kidney for his uncle. The FBI set up a kidney transport for Ari to rob, with Briggs help. If Briggs gets close to Ari it will lead him directly to the head of the family, Martun Sarkissian.
Johnny is still trying to close the Solano case and drives another cash delivery to Mexico. Carlito forces Johnny to eat with Lucia. She begs Johnny to kill Carlito, but he refuses. She grabs a gun and fires at her brother, but the gun is unloaded.
Rather than rob the transport, Ari kidnaps Sammy O'Malley. He has Tevan's blood type. Briggs signals for help several times, but the cover team doesn't show up. Ari puts Sammy in the trunk.
A police officer pulls them over. Briggs attempts to warn the cop, but the officer tases him. As the officer tases Briggs, he steps into oncoming traffic and is killed.
Charlie visits Mike in the hospital and tells him about Paige's meeting with Sid. Mike rips out his IV and tells Charlie they have to stop Paige because Sid will kill her.
Just as Sid is about to pull his gun on Paige, Mike and Charlie pull up and blow the operation. Sid sees Mike is alive and takes off. Furious, Paige tells Mike to stop saving her and shoves him. Mike tells Paige he forgives her.
Briggs awakens in a warehouse with Ari. He's harvested both of Sammy's kidneys. Briggs has no choice but to help Ari dispose of the body. They burn it along with the stolen car.
Sid's wife and child leave the country, but his whereabouts are unknown.
Briggs confronts Logan. He's convinced there was no cover team. Logan can't arrest Ari until they get Martin Sarkissian. Logan wants Briggs to be the fall guy. He'll be held accountable for Ari's crimes when the case goes to trial.
The team gathers at Graceland. Mike isn't cleared for duty, but he's back at the house full time. Paige put in her transfer papers.
Briggs returns and informs the team about the Sarkissian case. He reminds them it's the people who give Graceland its value, not the house. When one of them is undercover, the team is there to pull them back. To stop them from going too far.
Everyone starts cleaning the house, but Johnny receives a text and leaves. Johnny picks up Sid and they drive off.