UNIT uses (or has used) your base for an experiment involving troublesome alien technology. They might have once drilled into the Earth’s core and released poisonous gas, or weakened the dimensional barriers through out-of-control time travel experiments, or accidentally created dangerous alien hybrids. These experiments can – and will – cause problems for your base.
Side effects of the experiments make life on the base difficult or dangerous all the time, and sometimes they cause added problems.