The central mysteries of Dr. Brain resolve through several key narrative revelations:
- The Staged Death: Sewon's son Doyoon never died in the car explosion; his death was faked by Dr. Myung Tae-suk's syndicate to harvest the boy's brain, which possessed the same unique neuro-architecture as Sewon's.
- Jaeyi's Coma: Jaeyi refused to believe Doyoon was dead and hired investigator Kangmu Lee. When the syndicate discovered their investigation, Jaeyi was poisoned and framed as a suicide attempt.
- The Kangmu Lee Twist: Private investigator Kangmu Lee was murdered before ever meeting Sewon. When Sewon synced with a morgue corpse to follow a murder lead, he absorbed Kangmu's memories and personality. The Kangmu who actively assists Sewon throughout episodes 2 through 5 is entirely a post-mortem hallucination generated by Sewon's synced mind.
- The Mind Heist Climax: Dr. Myung attempts to permanently transfer his dying consciousness into Doyoon's brain. Sewon enters a simultaneous multi-person brain sync to infiltrate Doyoon's mindscape, where Jaeyi's comatose consciousness manifests to shield their son, purging Myung's psyche and allowing Doyoon to wake safely.