Fewer words will serve you better than more, for example; “…an ex CIA agent notorious for being the best they had…” could also be written as; “..a formidable CIA agent…” or “…one of the CIA’s former best…”.
The adjective notorious implies a negative connotation, but being the best is positive so a different adjective will do better here. “…stops at nothing…” is too vague unless you have some unique bit of action he will undertake it doesn’t help the logline and can be cut.

Here is a more focused version of your logline:
After his baby is kidnaped, one of the CIA’s former best agents must break out of an insane asylum to hunt down his own former student who took his daughter.