It's a rather long story, but the short version is that a very long time ago monsterkind and humanity went to war with each other and monsters lost very badly. The survivors were sealed beneath Mt. Ebott with a magical spell- anyone can come into the Underground, but only someone with a human soul and a monster soul can leave, and it would take the power of a full seven human souls to break the Barrier completely.

[Muffet answers in the calm, steady cadence of someone repeating facts she'd learned in history class at a young age.]

...If you meant 'why did they think it was a good idea to seal people under a mountain in the first place', your guess is as good as mine. This was all long before my time.