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When Danny realized that Rikki Sandoval stole his gun, he panicked. He knows he should report it, but at the same time, given what Rikki’s lost, given his own role in Ruben’s death, he can’t bring himself to ruin her life even more. While he hates that Ollie Barnes received bail, as a law enforcement officer, he understands that it’s not unreasonable for the charges that were filed. The robbery was the main crime, and Ruben’s death was, in the eye’s of the law, an unfortunate accident. And while the robbery was the secondary cause of Ruben’s death, Barnes isn’t the one that fired the shot that killed him, which means that there’s not a judge in New York that would have remanded the man.
Danny knows the key to finding Rikki before she can harm Barnes - and put Danny’s career at risk - is finding Barnes. As a detective, he has resources that Rikki doesn’t, which he hopes means that he’ll find Barnes first. When Lindsey starts calling him, he knows he should probably answer - make up some bullshit excuse about being sick - but he’s afraid that she’ll see through it and he’ll lose valuable time in his search for Barnes and Rikki - or even worse - that he’ll be forced to report the theft of his gun. What he doesn’t expect to for Lindsey to sic Flack on him. And while he’s far more comfortable telling the truth to his best friend than to his girlfriend, he doesn’t like the complications that it brings. Especially the clock that it puts on finding Barnes - and Rikki - before he’s going to be forced to report the theft of his gun.
Part of him feels bad about ignoring Flack’s calls during their hunt for Barnes given that his friend is helping him, but he also knows that Flack will track him down again anyway. That’s why he’s not surprised to see him as he steps between Barnes and Rikki. While his words - taking the blame for Ruben’s death - serve as a great de-escalation tactic, allowing him to get the gun away from Rikki and hand it to Flack, he also meant every word that he said. He was off-duty when the robbery occurred and Ruben was under his care. In that moment, Ruben should have been his priority, not the job. He’s tried to justify it several different ways, but he always comes to the same conclusion. If he had stayed with Ruben, the boy would still be alive. In trying to make up for the fact that the boy didn’t have a father, Danny cost him his life.
When Danny took Rikki home, he had every intention of calling Flack’s bluff to see if he would actually report the theft of Danny’s gun and the resulting incident. While Flack has a very strong sense of right and wrong - one of the things that Danny does admire about him - he’s willing to bend the rules in some situations, which he’s already proven once that day. It’s Rikki that convinces Danny to do the right thing, to take her to the station and get out ahead of everything. At her repeated emphasis that is wasn’t Danny’s fault, that the same thing could have happened even if Danny had stayed with him, part of him starts to wonder if maybe Rikki is right. The other part of him is telling himself that Rikki doesn’t actually believe what she’s saying - that she’s using the same de-escalation tactics that he used earlier. Attacking Barnes notwithstanding, Danny isn’t planning to do something stupid to punish himself for his role in Ruben’s death.
Given that he’s still mad at Flack over the fact that Rikki is facing criminal charges, he’s not going to tell the other man that he’s grateful that he took steps to make the process as painless as possible for Rikki. He only half means it when he says that Flack should have minded his own business - while the Detective’s involvement is the reason that Rikki’s about to be taken in front of a judge, without his help it’s possible that Danny wouldn’t have found Rikki and Barnes in time, in which case everything would be a whole lot worse.
Danny means it when he asks Flack how to stop blaming himself for Ruben’s death because he’s certainly tried. It’s while he’s on the way home that Danny remembers the other thing that Flack said. That being Danny’s friend made this his business. Danny’s been beating himself up over what he perceives as his role in Ruben’s death and keeping everything bottled up inside. What he’s forgotten is that there are people that care about him. People that he can talk to.
While Danny’s original plan was to go home and drink away his sorrows, he takes a detour and stops by his church. While he’s far from a good Catholic and doesn’t go to church nearly as often as he should, it’s a first step. He attends confession for the first time in longer than he cares to admit. While he knew better than the think that the act would solve all his problems, talking about everything with an impartial party that didn’t already the details of the situation did help. And prepared him for the next conversation he needs to have. He’s not sure how much Flack has already told Lindsey, but he knows that even if she is up to speed, she needs to hear everything from him.
When he gets home, he takes a quick shower to wash away the events of the day and then calls Lindsey. He can hear both worry and relief in her voice, but she doesn’t give away how much she knows, simply telling him that she’ll be over in twenty minutes. Even though logically he knows that she’s not going to judge him, it’s still the longest twenty minutes of his life. As he recounts everything to Lindsey - from retelling everything that happened on the day of Ruben’s death, to the way he’s blaming himself, to Rikki’s actions of earlier - she doesn’t interrupt, but simply holds his hand in support. He doesn’t know how long it’s going to take him to stop blaming himself for Ruben’s death, but for the first time he thinks that he’ll eventually get there.