The Aberrant War was a bloody conflict which was arguably inevitable. After a short "Golden Age," novas became increasingly violent and antagonistic towards humanity, as well as developing progressively greater physical mutations and mental aberrations.
Eventually the populace ceased to refer to them as novas, their heroes, and began to refer to them unilaterally as Aberrants. Although a few Aberrants remained on humanity's side, the majority of them were not.
Although tensions had been escalating for a while (see Feathered Serpent, Space Brigade, etc.), it wasn't until 2049 that war was officially declared by the United Nations. It was the first time the UN had ever officially declared war not on a nation, but on a race.
The Aberrant War came to a head in 2061 with the destruction of the OpNet by Mungu Kuwasha and the flooding of Florida by Poseidon. Finally, China gave its Ultimatum: it had several orbital platforms containing fusion warheads. All Aberrants were to leave Earth immediately or China would use the warheads to destroy the planet and everything on it.
So, led by Divis Mal, they left forever.