A protouniverse was a small, rapidly-expanding energy mass which itself contained a type of parallel reality.
In 2370, Jadzia Dax and Arjin, a Trill initiate who had been assigned Dax as his field docent, snagged a developing protouniverse after impacting a subspace interphase pocket while piloting the runabout USS Mekong in the Gamma Quadrant. As the protouniverse had become embedded in the runabout's starboard nacelle, Dax and Arjin brought it back to Deep Space 9 for study. Dax eventually discovered that the mass did not conform to their own laws of nature, and was displacing their own universe as it expanded. She also realized that the protouniverse displayed signs of containing life.
As the protouniverse was threatening the station as it expanded, the command crew faced a moral dilemma regarding whether or not they should destroy the universe in order to preserve the station and the rest of the Bajoran system. Eventually the decision was reached to return the protouniverse to the Gamma Quadrant, transported there by Dax and Arjin in a runabout. Traveling through the wormhole, they experienced difficulty in that, every time they passed through a verteron node, the protouniverse began to destabilize. Fortunately, Arjin, who was a level-five pilot, was able to successfully fly the runabout between the nodes, and the protouniverse was deposited back into the subspace interphase pocket. (DS9: "Playing God")