Gru is a supervillain determined to prove he’s the greatest by stealing the Moon. To pull off his plan, he adopts three orphaned girls—Margo, Edith, and Agnes—intending to use them as part of his scheme. However, as Gru bonds with the girls, his cold, villainous exterior begins to melt.

Queer Duck and his partner of 18 months (a lifetime in gay years), Stephen Arlo "Openly" Gator, hit a relationship crisis when the fey fowl is wooed by a brassy Broadway broad. Queer Duck wonders if he'd be happier being straight, while Gator the waiter spills his problems to a compassionate Conan O'Brien.

Colin MacLeod hunts for the man responsible for the death of his love. He chases the immortal Marcus Octavius across centuries as his quest threatens to take over his life and heart. In his quest, he meets a woman who reminds him of his slain beauty. But it's his final battle with Marcus that will decide not only his fate, but also the fate of everyone in the world.

The rats and mice, made intellectually superior in the original Secret of N.I.M.H., return to Thorn Valley to groom their destined leader - young Timmy Brisby.