"Aquarius" stars Grey Damon (left) and David Duchovny appear in the second episode of the NBC period drama. NBC

NBC’s newest crime drama, “Aquarius,” ended its premiere episode on a lot of intrigue and with a lot of loose threads left to tie up. Luckily, the second episode of the David Duchovny-led series picked up right where the action left off.

Thursday night’s episode began with detective Sam Hodiak (Duchovny) investigating a very personal case -- his missing son, who’s gone AWOL from the U.S. Army in the middle of the Vietnam War. He breaks into his ex-wife’s place, convinced that she helped him go on the run to parts unknown. He doesn’t find much to help his case, but he does find his partner, Detective Cutler (Chance Kelly), who has apparently been sleeping with her for five months. While it’s awkward, Hodiak says he doesn’t care and just wants to find his son, something he and his partner are on the same page about.

The next day, Hodiak and Shafe (Grey Damon) are talking at the precinct when they learn that one of the key players in Shafe’s ongoing undercover investigation was stabbed to death. In order to maintain his unofficial partner’s cover, Hodiak volunteers to investigate the murder. Unfortunately, by the time he arrives on the scene, Cutler has a suspect in custody, one who is willing to spill everything he knows about Shafe. Luckily for the seasoned World War II vet, he’s able to determine right away that Cutler has the wrong man.

Meanwhile, Shafe is still trying to get close to Charles Manson (Gethin Anthony). To do that, he once again enlists the help of Charmain Tully (Claire Holt). In the first episode, the two went undercover to try to convince one of Manson’s recruiters that she wants to be one of his girls. Unfortunately, the plan failed miserably. This time, they didn’t change the plan at all but it worked. Just like that, the two make their way to Manson’s compound and meet the man himself. It takes a lot of clever lies and some very unsavory deeds on Tully’s part to maintain their cover, but Shafe manages to get all the intel he needs to tell Hodiak where he can find his friend’s missing daughter, Emma Karn (Emma Dumont).

Soon after, Hodiak and Karn’s mother, Grace, go to the house where Manson’s followers are staying, only to find a cavalcade of drugged-out vagrants and neither Emma nor Manson. Following his very surprising affair with Grace’s husband, Ken, Manson extorted the $1,000 he needed to make a music demo, which he was off recording with Emma when Hodiak and Grace arrived.

Defeated and scared that she’ll never find her daughter, the two retreat back to Grace’s place. While there, the sexual tension between her and Hodiak finally comes to a head and they have sex. While the night ended somewhat well for Hodiak, Manson returns from recording and learns that a detective is on his trail. He hits Emma in the ensuing freak-out. In order to hide her, he offers her up as a “reward” to the guy who helped him record his demo. Emma will be staying with this stranger indefinitely, and it’s likely the last place anyone will think to look for her. The episode ends with Manson calling the Karns to torment them with the knowledge that only he knows where they can find Emma.

Tune in to episode 3 of "Aquarius" next Thursday at 9 p.m. EDT on NBC.