According to the TV show; the Omega 13 was a device discovered on an alien planet by Commander Peter Quincy Taggart and his crew. They apparently integrated into the systems of the Protector, but it was apparently never used during the show. The last episode of the show, in which the crew's ship was surrounded by enemies and about to be destroyed, Peter ordered the device be used before the series cliff ender and cancelation.
Galaxy Quest (1999)
The Thermians were known to have constructed the device aboard the Protector II; which possessed an unknown function to both the Thermians and the actors that starred in the show. There were believers who thought the Omega 13 was a matter collapser; which was a bomb capable of destroying the universe in a 13 second timeframe; however others; including Brandon, believed the device was a temporal matter re-arranger, which permitted the users a 13 second time jump to the past in order to repair a single mistake, which though insignificant in amount of both time and mistakes, could alter the course of events to great extent in the long run. It was known that it had power and energy to an impossibly extreme and unknown degree that some thought could be weaponized.
General Roth'h'ar Sarris' obsession over the device was started by the Thermian's former commander; who he tortured for information on the device's origin. He wanted the device for himself and requested it on his encounters with Jason and his crew. He even got to torturing Mathesar in order to get Nesmith to talk about what the function of the Omega 13.
Upon its activation at the end of the movie, the Omega 13 was indeed proven to be a matter re-arranger which helped Jason Nesmith stop Sarris, who was disguised as Fred, from killing the crew on the command deck.