The God That Will Come is a deity in several religions in the Space Stage. Followers of Spode despise this deity, and will immediately attack any of its followers. The only thing Zealots hate more than the "False" God That Will Come and its followers are the Grox. Shaman empires have made references to this god, mentioning that at least some of them worship it, and also suggest that the two religions are in conflict.
Very little is known about the God That Will Come and the religion surrounding it, other than that some members of Shaman empires follow it (as they mention in certain eradication missions). Zealot empires also mention the worship of the God That Will Come in their own eradication missions. In the latter case, the God's followers are violent extremists who try to kill the followers of Spode, although in the former case the roles are reversed.
According to the Scrolls of Faith (particularly Book 9), Zealots do not believe the God That Will Come to be an actual deity, but believe that he may be a demon. Possibly of note is a depiction in Book 9 of what appears to be a flying saucer apparently using an Abduction Beam, although any attempt to make connections between it, the God That Will Come, and any other things in the Spore Galaxy would be purely speculative.
Shamans also mention two other religious orders that they seem to be on good terms with - the Savvy Zxxon Monks (whom they call if the player refuses to participate in an eradication mission) and the Teachers Who Are Still Loitering Around (to whom you may be asked to give various Treasured Items). It is not clear whether these are religious orders worshipping the God That Will Come, or ones following different belief systems entirely.
The God That Will Come may also be a reference to the Christian God, due to the fact that it's said that he "Will Come" on the end of existence.