Perhaps the story could start with a glitch that transports some of the Undertale characters to the Little Nightmares universe. Papyrus, for example, might be completely baffled by the dark and creepy environment. He could try to befriend Six, thinking she's just a lost child. As for the Little Nightmares side, the Lady could see the Undertale characters as new specimens for her collection. This would lead to a battle of wits and survival between the two groups of characters.
A cool plot could be a character swap. Imagine Frisk from Undertale in the world of Little Nightmares. Frisk's determination would be put to the test in the nightmarish setting of Little Nightmares. They would have to face the Janitor and the Twin Chefs just like Six does. Meanwhile, Six could be in the Underground, dealing with Flowey and Toriel. The contrast in the two worlds' aesthetics and challenges would make for an exciting story.