This four-issue series, credited to "writer-penciller Phil Foglio and inker K.S. Wilson," never became part of DC's ongoing continuity for any length of time, despite its tying together three different DC franchises. I can't claim that APE II is any sort of neglected gem. Often it comes off like an unholy marriage of Roy Thomas (for continuity-linkages) and Alan Moore (inserting transgressive materials into kids' comics). Given that Foglio sports a comical bigfoot-style-- which is being applied to the silly, short-lived detective spoof from 1968--the humor is unusually shrill and, well, not especially funny. But APE II does make an attempt, however flawed, to follow through on the transgressive vibe I detected, at least in a house ad for the 1968 series.
APE II starts out with girl-on-ape violence.
For a moment, this seems like a sequence from the '68 series: a dizzy blonde girl detective messing around with her partner, talking ape Sam Simeon. One big change, though, is that, possibly in deference to feminist imperatives of the period, Angel O'Day becomes more of a tough, no-nonsense action-girl a la the heroines of Chris Claremont. However, while the original series never explained how Angel and Sam became partners in the first place, Foglio devises an origin. As a small child, Angel meets the talking gorilla on a safari in Africa, and somehow or other, Sam gets adopted into Angel's family.
However, Foglio decides that this family also includes Angel's half-sister Athena, a.k.a. "Dumb Bunny of the Inferior Five." My guess is that, because Silver Age writer E. Nelson Bridwell created INFERIOR FIVE and wrote stories for the '68 APE series, Foglio melded the two comic series with this maneuver. Thus Sam is raised alongside both half-sisters, who he regards as his real-but-only-figurative sisters. Athena, unlike Angel, is allowed to be somewhat like the dizzy blonde from the 1967 series, but with a more practical difference. Because she possesses immense super-strength, she's unable to have a physical relationship with an ordinary man. She tells her sister that she thinks she might be able to make Sam her boyfriend-- albeit a platonic one. (DC editorial probably said, "NO BESTIALITY.")
In the midst of this subplot, it's established that the reason Gorilla Sam has been able to walk around the city without (usually) being noticed is that he has some mental powers he uses to fool people. But something starts messing with the people of the city, turning them (temporarily) into a bunch of damn dirty apes. Plus which, Sam and Angel are attacked by a squad of super-strong humans, who turn out to be apes from Sam's old African haunts-- the Gorilla City of many FLASH adventures.
Sam, when told that Athena has a thing for him, is aghast, though Angel seems to have become somewhat more reconciled to the idea. Then, the mysterious boss of the ape-men stops by the detective office, puts Athena through a nightmare in which she kills both Sam and her father, and then introduces himself to all as Sam's grandfather, Gorilla Grodd.