I have a very different theory of the FS epos.
Long ago, the Universe was created by Us, the Gods. We created the Universe for the purpose of it creating Life. The Life which would grow in the Universe would evolve into Sentience. This Sentience was then able to ascend to a higher level - Our level, to stay by Our side ever wondering at the beauty of Creation.
Pretty religious, I know... now comes the fun part!
The Universe was given its own course of evolution, to create in it a sense of Near-Chaos, the ideal environment for Life. The randomness of its creation was left to the Universe itself. Everything went according to plan, except for a certain sector in the Brahma-mattercluster.
A mattercluster is what we now see as the Universe: a huge collection of matter that generated from a big bang. This mattercluster does have boundaries, and isn't the only one of its type. Many more matterclusters exist, pure nothingness between them.
Back to the story. The Brahma-cluster developed its galaxies at an unnaturel rate. While other clusters were still cooling off, Brahma was evolving much faster. This phenomena was not impossible, but the chances of it were practically nihil. The randomness that balances the evolution elsewhere was replaced by a terrifying perfection.
This perfect evolution led to the emergence of the Narvanii, a great, sophisticated race which developed the technology for Artificial Sentience. They created a project called 'Shiva', to end a war between three other species not far from their fragile civilization. They designed Shiva as a sort of supercomputer, destined to end all wars.
There you have it - I see the Shivans as a race of artificially intelligent machines which has a perfect understanding of the Universe. Every possibility was calculated. The Shivans were impossible to defeat, as they were perfect. It would take something impossible to take them down!
The Shivans were designed to end all wars. Unfortunately, the mere usage of subspace was designated as an act of war by the Shivans, so the Shivans spread out and killed everything everywhere. The Shivan Empire became so vast, and its grip on the Universe so unbreakable, that We, the Gods, had no alternative than the Dissolution of the Universe.
As we created the Universe, now we began with the undoing of it. Entire clusters were reduced to nothingness, and the Shivans along with them. This dissolution was coming to Andarta, the home-cluster of the Terrans and Vasudans - and it's the bigger problem the Shivans are the symptom of. In Capella the Shivan J-fleet created an inter-cluster jumpnode to escape the Dissolution. The GTVA has to do the same... or they will be de-rezzed!
I'm still working on the story, and I've got a detailed (and far better IMO) version of the story above. I'm putting it all in respect with the events of FreeSpace, the T-V War, the Hades Rebellion, Aken Bosch, and the destruction of Capella.
Tell me what you think!