Santo vs. the Diabolical Brain aka Santo contra el cerebro diabólico has no connection to the Evil Brain that Santo battled in 1958. Instead it is the first step into having Santo carry a film rather than the plot device who saves the day.
The film opens with police detectives arresting a mysterious criminal who is never named and never speaks, but who is apparently a subordinate of a criminal mastermind they hope to catch.
The first part is never mentioned again, and at no point is anyone resembling a “cerebro diabólico” (diabolical brain) ever seen. I have to assume that for one reason or another they abandoned the original story for what they ended up with, but the result is a pointless and confusing prologue and a title that doesn’t make any sense at all. But in the end, who cares? It’s El Santo!
In the second part, Fernando discovers that Virginia has gone to an isolated village to do a story and disappeared. The detectives go after her and find a small community lorded over by a rich and evil man in a pretty typical Western genre plotting device.