We pick up from where we left off last season with Horatio racing to MDPD when he figures out, from serial killer suspect Bob Starling's recent clue, that something bad has happened to H's. He arrives to discover that everyone is passed out from a foreign gas that was pumped through the lab. Everyone gains consciousness except for Jesse who fell from passing out and hit his head causing his death. The team cleans up the aftermath and watch in shock as Jesse's body is taken out on a gurney. Horatio and the team will not stop until they get Starling for murdering Jesse. They have Starling in custody but are unable to actually charge him as all the evidence from his previous kills are contaminated from the gas leak. Natalia calls Melissa Walls, his PhD student, hoping to get her to help us but she seems oddly dismissive and says she wants nothing to do with Starling. From examining the "All Fall Down" note which Starling left for H, they link the ink and paper to Starlings inkjet printer. They discover the Halon gas tanks left by the air conditioning vents on the roof of MDPD that were used to knock our team unconscious.
The tanks are traced back to Dade University where Starling recently worked at. Meanwhile back at MDPD Starling taunts Horatio by being able to free himself of his handcuffs and tells H that the "clock is ticking". H tells Tripp to transfer him to the maximum security prison in Miami. While Walter is cleaning up Jesse's face and saying his goodbyes he finds a shard of glass in Jesse's wound on his forehead. We later find out this glass is from a broken LCS screen on a digital camera. Walter searches for the memory card that Jesse was trying to download. Based on the timing of events they conclude that someone on the outside was helping Starling pull his plan off. They go to find Melissa, the obvious accomplice. As they are about to open her door they discover that she's been tied up and opening the door will trigger a gun pointing at her to go off. They get around it and save her. They trace the bullet to a gun that belongs to Keith Garwood, the janitor at Dade University. Keith also has access to the storage closet that housed the tanks of Halon. Keith pleads that he had nothing to do with the Halon gas or tying up Melissa and rigging a gun at her. Calleigh inspects the bullet from the gun in Melissa's apartment and discovers that it is filled with sand and not gun powder which would have prevented it from going off. Through additional inspection of the "All Fall Down" letter they discover a hidden message in invisible ink that says "Man marks the earth with ruin, but his control stops at the shore". Horatio remembers Starling telling him "the clock is ticking" and puts it all together. H and the team race down to the beach and discover an unclaimed cooler with a ticking clock in it. At the same time Starling is being personally escorted by Tripp in a green and white van to maximum security prison. Within a matter of seconds gunfire from out of nowhere starts pelting Tripp's car causing he and the officers to run for cover. Starling is able to free himself of his restraints and escapes unscathed. Meanwhile, Walter and Benton try recover erased pictures from the memory card only to discover intimate photos of Starling and Melissa. They were in love and she was his accomplice. She planted the gas at MDPD and she tied herself up and framed Keith Garwood. They bring Melissa into custody and she agrees to cut a deal in order to avoid the death penalty. Melissa meets Starling at the marina as they had planned, and wearing a wire she gets Starling to admit everything he has done; all the evidence they need to convict Starling of Jesse's murder. The uniforms take Melissa and Starling into custody.