Season 2 Episode 1 "Human Traffic"
Deeks was missing. Their LAPD Liaison had failed to check in while on an extended undercover assignment. His prime suspects had been killed in a car explosion. Then his case handler had been killed too. His fellow detectives were quick to write him off as well. When he regained consciousness after nearly being blown up himself, he knew there was only one person to call, Hetty Lang.
Although he had only worked two cases with them, he felt safer with NCIS at his back than with his own department. After talking to Hetty, he had persuaded her to allow him to go back in and try to close the case. As usual, Deeks was undercover alone, so when Lazik had called him by his real name he thought it was over. He could see no way of getting out of that power plant alive.
Then Callen came walking in like he was there everyday. It took all of Deeks' strength not to smile. After the bullets stopped flying, he told them about Traynor and her cousin. Without hesitation they believed him. It was just a matter of getting Scarli to show his true colors. When the traitorous detective insulted the closest thing Deeks had had to a partner in a very long time, all he could think about was that this son of a bitch would continue to draw breath while Jess was dead.
Later that night as Deeks laid in his bed staring at his ceiling unable to find sleep, he wondered, "What would I have done if I had been on my own like usual?" It would have been so easy to pull that trigger. Having Sam, Callen and Kensi there had saved more than one life. As he closed his eyes he realized that he may have finally found a home at NCIS.