The one you were thinking of is Season's Greedings. Toy Story (guest starring the boss guy from Murphy Brown) is the second to the last episode of the series where a disgruntled scientist kidnaps orphans and kids of his former employers, using a transporter-like device.
He kidnaps Dr. Klein with toy soldiers and a duck. He tries to kill L&C once with a duck and blows up his own toy store with Clark in it with another duck.
Lois is kidnapped instead of a child and ends up telling all the kids a story about a scared little baby who ends up being Superman. She then realizes she wants children of her own, after all.
