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Doggett: Protecting? How, by getting him locked up in prison in the first place?
Reyes: So either he's doing Fassl's bidding, or Fassl's doing his.
Robert Fassl (W. Earl Brown), a serial killer who Doggett helped put away back in his NYPD days, is released after fresh DNA evidence exonerates him. Scully notes that although the DNA doesn't match Fassl, it suggests the actual killer was a blood relative — which is odd, because Fassl has no living blood relatives.
- Broken Pedestal: John learnt important tactics from his old NYPD partner, Duke, such as not giving up on a case until one is completely certain they did everything they could. This is shattered after he finds out about Duke's planting of evidence in the Robert Fassl case.
- Disappointed in You: Doggett informs Duke of this, since he found out that the latter planted Robert's hair at the crime scene in the opening flashback, so that an arrest could be made."Duke, you son of a bitch! THIS IS A FELONY! I don't know how I can forgive you for this! You break my heart."
- Double-Meaning Title: The episode title "Underneath" refers to the sinner side submerged underneath Robert's normal personality. It also refers to the victims Robert or rather his vengeful personality has killed and buried underneath in the sewers.
- Downer Ending: Reyes had to shoot Robert's sinner side to save Doggett. Unfortunately, it has the side effect of killing Robert as well. The police swarm the sewers to find the remains of Robert's victims, confirming that he truly is a reluctant killer. As for Doggett, he is still reeling from learning about Duke's corrupt act, and cannot comprehend the case's ending.Doggett: I can't accept this. If you can, God love ya, but, it's not the way my mind works.
Reyes: You closed this case. This time around, that was enough.
Doggett: What happens next time?
- Flashback: At the beginning of the episode, it jumps back 13 years ago to Robert being caught red-handed in a murder by two cops. One of them was Doggett.
- Frame-Up: Doggett's partner put fake DNA to convict Robert since he found no real evidence of him.
- Mirror Scare: As Jana tends to a head wound of Robert, we see the two in a mirror as she opens it. Grabbing some ethyl rubbing alcohol and bandages, she closes the mirror and is shocked to see a different man behind her, instead of Robert. This can be seen in the page images.
- Split Personality: Robert has suppressed his sinner side so much that it manifested into a literal split personality which kills with no compunction.
- Tragic Villain: Robert is a good man struggling with an evil, murderous split personality.