Building on my theory that QA and Shaper are busy building a new type of shard from scratch, I think that the Newtype shard will be truly symbiotic in nature, bonding with a human, uploading them to the shard-cloud without a conflict drive. The Newtype, through some combination of pinging or being aware of things through the eyes of its parent, will know of the naked singularity tech, thus eliminating the entire point of the Entities.
The birth of the Newtype will get Scion's attention, Scion will try to reap it to gain the knowledge of [INFINITE ENERGY], but because Shaper and QA made it using their unprecedented interaction, it won't answer to Scion, kicking off the End of the World as Scion throws his tantrum.
Stuff happens, a lot of people die, Scion works intelligently to maximize the damage to the rogue shards/parahumans and destroys all backups of Pantheon, actually giving us a cause for narrative tension again. Taylia and most of the cast die, but Newtype, in a display of filial piety, teams up with Dragon and we get an epilogue a few years later where they have managed to recreate the cast through Spacewhale and Singularity magic.