The Program

How did the Deviants and the Vagrants come to be, exactly?

Well, the answer is simple.

The area, the island in which they're all fighting is a giant program.

This program was made many a millenia ago, by a race of people older than the Zarathustrans. The program exists to make a carbon copy of the universe as a fallout shelter, minus all of the people. Silver Hood abuses this program to kill people. Simple enough.

The Deviants accepted Silver Hood's invitation and entered the program, but, as everything must come at a cost, the program did something bad.

It started to create tears in other parts of the universe. Eating matter and flat out destroying humanoid/xenomorphic life, several indiviuals considered this a threat to their planet's safety, and hopped in.

These people. Are the Vagrants. Silver Hood didn't expect anybody to notice, find, or even go through the tears, but some foolish people did, and the epic clash of the universes, grew in size. To ensure the threat be dealt with, Silver Hood declared they were rogue enemy programs that had to be deleted. And thus our feud comes full circle.