Why was Shakespeare's theater closed for a few years?

Theatres in Shakespeare's day were frequently closed for health reasons, to prevent the spread of communicable disease (to wit, the pneumonic plague). The longest such closure happened around 1593-1594 and was so severe that it bankrupted a number of theatre companies, who were forced to reorganize with new patrons. At this time Shakespeare was not associated with any theatre, but it didn't matter, since all the theatres were treated the same.