Commodore April, in a shout-out to Gene Roddenberry, and his wife are aboard visiting when an alien ship tries to fly into the Beta Niobe nova (remember them?). So Kirk tries to stop them, which he can't, and ends up with the Enterprise getting dragged in as well. Not a healthy place to be. Somehow, they survive entering the nova. Now they're in an Oreo milkshake.
Everything is working in reverse. Sarah April's dead flower regenerates itself. Everything works in reverse, in fact. They're even de-aging. Hey, wasn't that the final episode of Star Trek: The Next Generation?
They even fly backwards. They have to find a way to get back to their universe. They find some people who age backwards. Hey, wasn't that an episode of Star Trek: Voyager? Anyway, together they figure out a plan to get back. Everyone starts de-aging and forgets how to use their consoles which is mildly amusing. April uses the Transporter solution from "Unnatural Selection" to make everyone grow up again.
And that was the end of Animated Star Trek.