Henry finds out that Jordan was married to Ida for a short time in the 90's, so they go to Ida to press her about Jordan. Ida explains they broke up because she wanted kids and Jordan literally could not produce them, as he was and still is sterile. From this they determine that Jordan could not have been the one who impregnated Veronica.
Just then, Shawn remembers he saw a business card for an OBGYN found in Veronica's belongings that has now been noted as evidence. They go to the OBGYN's home and find out that he did in fact deliver Veronica's baby, but didn't know who the father was. The only thing he knows is that the baby was named Dahlia Towne.
After Gus drops Shawn off, Shawn is immediately accosted by a man in a ski mask. He gets knocked out, but is OK the next morning.
Shawn and Gus show up at Thea's room at The Beaumont Hotel demanding to know where Jordan is. It turns out Jordan is there in Thea's room. They question him, but Jordan denies ever trying to threaten Shawn. It wasn't Jordan who accosted him in a ski mask the night before.
Just then Shawn gets another mysterious threatening call. Lassiter, who had a tap on Shawn's phone, calls Shawn immediately after and tells him that they traced the mysterious call back to a payphone two blocks from where Shawn is. Shawn and Gus are able to make it to the payphone in time to see that the same person who made the calls and who is currently fleeing the scene, is Jack, another one of Henry's former co-workers who was on the Veronica Towne case years ago.
Jack is brought into the station for questioning and admits to taking part in the drug scheme at The Blue Derby, along with Lou who was hesitant at first to participate. He goes on to tell them that Ellis called them and told them there had been an "accident with one of the Blue Derby waitresses" and that if they didn't play a part in covering up her death, Ellis would expose the fact that members of the SBPD were taking bribes. Lou was the one that hid the body, but felt guilty about the whole matter and threatened coming clean about the whole thing. But even after all of that, Jack still vehemently denies killing Ellis. Suddenly, Shawn notices in Ellis's file that he was colorblind. This prompts Shawn to flashback to a moment that makes it clear that Thea is colorblind as well.
From this, Shawn discovers that Thea is actually Veronica and Ellis's daughter, who was adopted after Veronica was killed. Her adoptive parents changed her name from Dahlia to Thea. And Jordan is actually Thea's brother.
Shawn and Gus pay a visit to Thea who is in the midst of leaving town. Jordan is there too, pleading with her not to leave. Shawn does the case breakdown right then and there and tells Thea and Jordan that Ellis (who was married at the time) knocked up Veronica, sent her away to have the kid, and when Veronica returned after giving birth wanting more from Ellis, he choked Veronica, paid off the cops to cover it up, and sent Thea off to live with her adoptive parents. But years later, Thea's adoptive parents told her the truth about her real mother that went missing 20 years ago, and shortly after, Thea moved to Santa Barbara to investigate for herself. And when Thea discovered the culprit was Ellis, she had him bring her to the same site where he killed her mother and shot him in cold blood. Thea is then arrested and placed into police custody.
The next day, Henry turns in his gun to Chief Vick, telling her that he is through with police work, as this news about Lou and Jack really shook him. He also tells Shawn that he wants to take time away from The SBPD to spend more time with Shawn. Henry offers to grab a beer together. Shawn agrees, but Henry says there's an old friend he needs to visit first and that he will meet up with Shawn after.
Henry shows up to chat with another former fellow cop from 1991, Jerry, who was also on the Veronica Towne case. Henry laments about everything that went down with Lou and Jack. Then suddenly, Jerry slips and accidentally admits he was a part of the police cover up about Veronica as well.
Back at the SBPD, Shawn realizes that the old friend Henry is visiting with is Jerry after he sees a file saying Jerry was also part of the police cover up. Shawn's face drops, and immediately goes to find Henry.
However it is too late, as Jerry has already pulled a gun on Henry and has shot him point blank.