I consider the Transcendentals to be a multiple Dataform. So you start building Transcendentals with multiple metatech virii in order to slowly warp their worldview into eventual suicide. Multiple, because the Transcendentals should be powerful enough to take on a single infected Transcendental. Ingame, this could be shown over multiple games with the Transcendentals slowly going strange, with a vista beyond which they cannot see approaching, which would be their death. In order to avoid new Transcendentals, a salted earth technique is taken on, either through a machine that builds infected Transcendentals ad nauseum, or, by the infection leaving a "taint" that infects subsequent Transcendentals. And voilà, Transcendentals removed during a game.
Ooh, that's a neat idea. If the Transcendentals are actually Multiple, they would expect some kind of disruption in their communication when they absorb new minds, so they might not be able to get the information that tells them these new T's are infected.