What I think you're referring to when you say the AI/scourge is debris, which is generated on explored worlds you don't own when you build a new city. The results vary somewhat - the marauders and AI factions taking debris is not really that much of a problem and has little real effect, while the macrophage taking one has a very significant one-time effect, the nanocaust taking one is something to be scared of, and the scourge taking one is a "Oh god, oh god, we're all going to die" level of severity.
For the marauders, nanocaust and scourge, it permanently unlocks new ship types for them, but the marauder ones are actually not really much nastier than their existing stuff IMHO, while the scourge spire hybrids are just death incarnate. Meanwhile, the macrophage one spawns what I would describe as a fallen spire scale version of the devourer golem - it's immensely powerful, but slow. The generic AI factions spawn a spire cruiser into the threafleet.
The AI can also take actual shards, via relic trains reaching their destination - this spawns a mk1 spire battleship (IIRC) into the threatfleet, but because it's only Mk1 it's not really that threatening.