There is no real story behind and if you've played the MSF way in SW2 you wold knoe that the Angorian-Race was killed completely (so told by story) maybe ther some survivors or something else.
But there in my memory 3 story-lines in SW2 (spoiler-warning):
in one EL coming and take the super-angorian weapon and destroy humanity with it
in one other the energy output of the super-angorian weapon is used to build a huge laser so the concern of SW2 can control all
in the last (already say over the spoiler) the MSF sends the super-angorian weapon (its a bomb to let the cat out
) as a missile back to them trough a portal and they get destroyed
so see the missery there so uncompatible story endings like in SW3CW that the story has to been rolled back and to say it was so in the end ... because what would you make with these 3 endings from SW2 to SW3CW
i would think the only where to let the player choose or let them jump so each sector has its own paradoxon
the same would it be from SW3CW to SW3AoV you can't build on all endings on the same time ... so angorians away nothing left of them and over