Despite the pressure, Deeks notably leaves the papers unsigned at the end of the episode, choosing to remain a Liaison for several more seasons.
The shooting was actually faked to get Deeks back into the LAPD undercover to find a mole. Ncis Los Angeles 3x10
LAPD Lieutenant Bates acknowledges that Deeks has found a "home" with the NCIS team. He encourages Deeks to finally sign the papers and make it official. Despite the pressure, Deeks notably leaves the papers