Of the course the Shivans didn't just run away. I personally think that the Shivans did their job, and, once it was completed, left.
Take a look at when and why the Shivans have or would have come. Freespace 1 took place at the beginning of the fourteenth year of the T-V War. Heavy casualties have been inflicted on both sides of the conflict, and then, without warning, the Shivans arrive and begin to devastate Terran and Vasudan forces on all fronts. As the Terrans and Vasudans bind together to fight the Shivans, another force arrives--the Hammer of Light. At first, the Hammer of Light composes possibly a significant portion of the PVN fleet and continues to disturb the fragile GTA-PVN ceasefire during the Great War.
The Shivans level Vasuda Prime and finally move on towards Earth and Sol. At the same time, Ancient records in Altair are discovered, and at about the time of the recovery, the HLD Anvil, a Hammer of Light flagship, is destroyed by the recovery group. Shortly thereafter, the Terrans and Vasudans destroy the Lucifer in subspace, sealing the jump node to Sol and ending the Shivan invasion.
Why did the Shivan come during the T-V War? I think simply to end the conflict between the Terrans and Vasudans. We know that the Shivans have opposition to races using subspace to expand and/or wage war--this is evident with the Ancients' empire. Noticing that a war had broken out between two subspace-faring races, the Shivans were awaken and arrived to end the conflict by whatever means necessary--by unifying the races, or by completing wiping them out.
Thanks to the Hammer of Light and their continued crusade against the GTA and PVN, the Shivans did not halt their attacks--they instead destroyed Vasuda Prime and moved on to destroy Earth. After the destruction of the Lucifer, the Shivans possibly remained for a while longer. As the Hammer of Light (and the new Hades Rebellion) was whittled down and made more and more powerless, I would assume that the Shivans would have eventually begun disappearing here.
In FS2, after about thirty years of peace between the Terrans and Vasudans, the Neo-Terran Front forms and rebels against the established GTVA. A couple of years into the rebellion, Admiral Bosch sends the NTC Trinity to activate the Knossos portal in Gamma Draconis. The Shivans arrive again, and penetrate all the way to Capella. At the same time, Admiral Bosch initiates his first contact with the Shivans. Shortly after, the Shivans cause the Capella star to go supernova, ending the Second Great War.
Why did the Shivans come the second time? Two reasons, possibly--the NTF Rebellion. Just like the T-V War thirty-two years ago, the Rebellion pitted two powers against each other in a costly war. The death and the use of subspace again to transport warships through to battlegrounds would likely have been enough to bring the Shivans back.
Secondly, the possible activation of the Knossos could have triggered some subspace disturbance--a loss in the equilibrium of subspace nodes in the sector of the galaxy. The Shivans return, and, since the Knossos portal had stabilized by the time the Shivans were pouring into Gamma Draconis and Capella, there was nothing the GTVA could have done to collapse the extremely powerful vortex connecting possibly one section of the galaxy to another.
When Admiral Bosch makes contact with the Shivans, the actual Shivan offensive appears to turn towards mostly toward the Sathanas juggernauts. As the 80+ Sathanes close in on Capella, the GTVA begins to evacuate and prepares to shut down the two nodes GTVA-controlled nodes at Vega and Epsilon Pegasi. The Shivans cause the Capella supernova through an unusual subspace disturbance just as the Nereid collapses the jump node to Vega.
The loss of equilibrium in the subspace nodes in the Gamma Draconis sector through the activation of the Knossos could have caused the Shivans to want to destabilize other nodes to restore the balance. As we said, we can't apply human characteristics to the Shivans, so it is possible that the Shivans were more than capable of realizing that the GTVA would have discovered some way to stop the Shivans if they were faced with an unstoppable juggernaut force--collapsing the nodes.
My theory here is that when the Shivans destroyed Capella and created the unusual subspace disturbance, it may have either permanently sealed what the GTVA had done to the Vega and Epsilon Pegasi nodes, yet generated just a stable enough vortex for part of the juggernaut armada to jump out once the star had been destabilized enough. Thus, the balance is restored: the loss of two or three nodes in Capella may have balanced the subspace force as the Shivans would have come for. Without an NTF Rebellion or major conflict to deal with, the Shivans were focused more on the subspace nodes, and not ending a conflict, as they could have intended early on.
So, summary: The Shivans are the Great Preservers and an intergalactic police force. They monitor subspace equilibrium and control intergalactic disputes through their own methods. The Shivans are not a stationary species bent on expansion and conquest, but only appear when a problem must be dealt with.
Argue, please.
