Cut to later, with the whole team giving a rundown of the cold case behind all this: The discovery of the abandoned body of a 14-year-old rape/murder victim named Alisa Hernandez, last seen leaving school with BFF Cecilia Cruz, who claimed they split up before any raping or murdering occurred. Fielding thinks Cecilia was lying, and more to the point, she suspects Kralik of being Alisa's rapist and killer. Munch declares that if they can prove Kralik did it, Chester's off the hook. Seems like kind of a leap, but we've got a lot to get through in this hour.
Munch follows a uniform through an evidence warehouse to a ten-year-old rape kit. It's in less than mint condition, and it already has two pending requests logged, the requestors being none other than Chester and Detective Kralik. Suffice to say that Munch pulls rank -- Cragen's rank, to be exact -- and leaves with the sample.
Fin meets Fielding in a diner so she can offer her help, provided Fin can get her the ballistics data and that fancy 3-D scan of the crime scene. Fin tells her they've got that covered, but she's not convinced that'll be enough to clear Chester in time, or indeed at all. She senses Fin's irritation with Chester for being so secretive, but when Fin asks her for a possible contact, she names his ex-partner, Wesley Meadows.
Olivia and Elliot are the ones who catch up with Meadows, a dapper fellow who agrees with Fielding that Cecilia Cruz was full of it, and was likely raped as well on the day of Alisa's murder. Not that they could prove it. But at least he gives them a lead to finding the dead girl's father.
Which they do, and he's pretty bitter about losing his family, though when they tell him that Chester might have solved the case, he perks up. Still, he doesn't believe that Cecilia was holding out on them, until Olivia says Cecilia was raped too. A surprised Hernandez wonders why Chester didn't mention this when he called him last night, asking to talk to Cecilia. Oops. Olivia and Elliot follow Hernandez's directions to a clothing design shop downtown, only to find out that Chester took her out of there the night before, leaving a fair amount of his blood behind on the floor. On their way out, Elliot sums it up: "She's now his hostage."After the break, Olivia, Elliot, Cragen, and Fin all conference tensely into the squad room, sniping at each other. They really need an interesting clue to distract them and calm things down. Fortunately, right on schedule, Munch is waiting there with a big video display and a ballistics guy. They report, among other things, that there was a third shooter on the scene who also had a police-issued weapon. Replaying the scene, the ballistics guy demonstrates how Chester's first two shots spun Kralik and the last three hit him in the back as he was falling, which proves that Chester didn't open fire on Kralik's back. Chester then fired in the direction of the unknown shooter, who left no evidence behind other than two bullet holes clear through Chester's arm and leg. This prompts the group to theorize that Chester took Cecelia in order to protect her from the unknown shooter. So who's the third shooter? Olivia and Elliott decide to visit Kralik's widow to ask if her dead husband had any friends on the force who might be rapist/murderers/attempted cop killers like Kralik.