This article contains spoilers for Stranger Things season 4 volume 1.
CIA's Project MKUltra program.
Dr. Brenner was initially believed to have been killed by the Demogorgon in Stranger Things season 1, but in season 2 Eleven learned he had survived. A former orderly at Hawkins Lab claimed he could take Eleven and Kali (Linnea Berthelsen) to Brenner, a comment that strongly implied the scientist was still working with the CIA in some capacity. No doubt Kali has spent the last two years looking for him, but Eleven decided she had better things to live for than revenge and committed to her friends and found family instead. Brenner's whereabouts have remained a mystery until Stranger Things season 4.
Stranger Things season 4 revealed Brenner not only survived the Demogorgon attack but did so unscathed because he appears to have suffered no serious injuries. He presumably reported everything that happened at Hawkins Lab, including Number One's massacre and the release of the Demogorgon, to his superiors. This probably means Brenner was working with Sam Owens (Paul Reiser), the man who took over Hawkins Lab, all along.
After the events of Stranger Things season 1, the CIA set Dr. Brenner up at a secret lab in the New Mexico desert, in a repurposed storage silo that used to contain ICBMs. There, Brenner continued his research, presumably now focused on trying to figure out how the Hawkins Gate had been created. He was clearly helped by extensive security footage from Hawkins Lab, which showed Number One's slaughter of the test subjects and his final battle with Eleven. Brenner and Owens appear to have believed the various incursions from the Upside Down were a hint of what was to come, considering Number One to be a major threat. It's interesting to note that Owens carefully said the base was repurposed "to hold something much more powerful than a missile," as in Eleven, which means it was also likely fashioned to contain Number One.
Dr. Brenner's focus changed when Eleven lost her powers. According to Owens, the entire project dedicated itself to figuring out how to bring back Eleven's powers. Dr. Brenner theorized that the injury Eleven sustained from the Mind Flayer was comparable to the impact a stroke can have on some individuals, with Eleven's brain no longer connecting properly. He established the Nina Project to help Eleven re-experience her memories and restore her powers. Stranger Things season 4, volume 1 seems to end with the success of the Nina Project, which means Dr. Brenner has restored the only being who can stand against Number One.
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