From the show's tvtropes page:
Bureau of Alien Detectors, or B.A.D., was a 1996 animated series.
In it, aliens have invaded the earth. A carefully selected and trained group of five people called the Phalanx Squad, monitor, control, and battle the alien visitors.
But some people in the Bureau may have hidden agendas of their own concerning what to do with the aliens.
The episode you remember is "And Then Comes the Rain". Watch that below: