Woolie Wool's theory

Note that this is derived from an intelligence entry written for a mod set in the year 2393.

Origins

The Shivans originated around 40,000 years ago near the galactic core as an intelligent, terrestrial species on an Earthlike world that has long since been completely sterilized. Mere decades after building their first rocket-powered orbital spacecraft, the Shivans discovered subspace, along with two interstellar nodes in their home system. The Shivans developed subspace technology with similar speed, and within a few centuries had holdings in thousands of systems. With an ever-expanding empire and no other sentient races yet discovered, the Shivans saw themselves as the destined masters of the universe.

Exodus

Then, around 28,000 B.C.E., the Milky Way galaxy was invaded by an imperialist power that the Shivans called "Tsi-Ka", or "Aggressors". The Tsi-Ka immediately attacked the Shivan empire, destroying much of the Shivan navy and subjugating Shivan worlds, setting up duchies run by high-ranking Tsi-Ka on each world and deploying billions of foot soldiers from thrall races under their control to subdue the civilian population. The Shivans fought relentlessly, but each battle saw another world lost.

In desperation, the Shivans collapsed the Gates, the huge subspace nodes linking the Milky Way to other galaxies, sealing the Tsi-Ka invasion force off from reinforcements, but it was still not enough. The turning point came when Shivan scientists developed a protective particle sheath that could be projected around a starship—the first shields. Shielding technology was only compatible with ships of fighter size, but it made Shivan fighters nearly invulnerable to Tsi-Ka weaponry. Although they now dominated the Tsi-Ka in space, they repeatedly failed to win back their worlds from the Tsi-Ka and their thrall races, which had overrun all of their core planets.

The Shivans saw only one way to cleanse the Tsi-Ka threat forever. They developed a new weapon, the particle beam cannon that is ubiquitous in modern naval warfare, and mounted two of them on an enormous new starship class, the type of ship that the human race would millennia later dub Lucifer. The Shivans deployed several Lucifer-class ships, and using their beam cannons, bombarded their own planets until every trace of life had been exterminated.

Great Destroyers

The war was won, but at a terrible price. The Shivans had lost their planets and most of their resource base. Seeing fixed habitats on planets as a liability, they began a genetic alteration process to adapt their bodies to zero gravity environments in the depths of space, and to make every Shivan a match for a swarm of Tsi-Ka soldiers. The Shivans became hideous, colossal black creatures, infused with cybernetic weaponry and countless augmentations, almost unrecognizable from their original forms. Their Lucifer-class ships, and the later, larger Sathanas-class vessels replaced planets as their homes. The Shivans became nomads, wandering throughout the galaxy in vast fleets of starships and occasionally stopping to collect resources. These were the Shivans that would bring doom to hundreds of worlds.

Paranoia set in, and the Shivans were determined to let no race ever threaten their existence again. They developed sophisticated technology for tracking subspace jumps, and as soon as they detected significant subspace activity, they would snuff out the source. Countless races were purged from the galaxy by the Shivans. They even developed shielding for their Lucifer-class ships, a technology we have never been able to replicate. The Shivans became the Great Destroyers of legend.

But success breeds arrogance and complacency, and the Shivans developed what seemed like a surefire method of victory. They would send a small strike force, spearheaded by a single Lucifer-class vessel, to dispose of the enemy species with the minimum of effort or expended resources on the Shivans' part. Secure in their own supremacy, they let their technology and tactics stagnate, falling back on crushing strikes with a single Lucifer-class ship and a skeleton fleet time and again. This was a trait that would bring their reign of terror crashing down.

In 2335, the Shivans came for us, invading the Galactic Terran Alliance and Parliamentary Vasudan Empire from several systems, including Ross 128 and Ikeya. Weary from fourteen years of warfare with one another, the two young empires formed an alliance of convenience to defeat the Shivans. At first the Shivans seemed invincible, the Terran and Vasudan weapons useless against their shields. But unlike other races before them, the Terrans and Vasudans, working together, turned the Shivans' own technology against them, reverse-engineering Shivan shields, sensors, weapons, and other technologies and adapting the subspace tracking technology previously reverse-engineered by the Ancients. In the subspace corridor between Delta Serpentis and Sol, ships launched from the destroyer Bastion destroyed the Lucifer, breaking the back of the Shivan offensive.

Stunned at their first defeat in thirty thousand years, the Shivan retreated, quickly mobilizing and militarizing to deliver completely overwhelming forces to crush the Terrans and Vasudans. With a fleet of over one hundred enormous Sathanas-class juggernauts and over 250 other warships, the Shivans overran the frontier of the now permanent Terran-Vasudan alliance within weeks. But on the eve of ultimate victory, the Shivans did something that still confuses xenologists today.

When the leader of an anti-Vasudan rebel faction, Admiral Aken Bosch, used his ETAK prototype device to contact the Shivans through their own language and protocols, the Shivans responded in force, but instead of destroying his flagship Iceni, they boarded his ship and abducted him and his command staff. Instead of using the Sathanas fleet to reduce every world in the Galactc Terran-Vasudan Alliance to ashes, they brought the ships into orbit around the star Capella, using their other ships to divert the GTVA away from their juggernauts. Over the course of three days, the Shivans used advanced subspace devices to create what scientists now believe was a temporary Gate around the Capella star. As they jumped out to parts unknown through their Gate, Capella went supernova, annihilating the dueling GTVA and Shivan fleets in the system. The Shivans were never seen again. Admiral Bosch was discovered in a Shivan fighter in the Vega system, but he self-destructed his ship before GTVA forces could arrest him.

To this day, Terran and Vasudan ships carry ETAK devices as part of their comm suites to communicate with the Shivans in case they ever returned, but they have yet to do so even after nearly thirty years. Whether or not they will ever appear in Terran-Vasudan space again, or whether their intentions will be friendly or hostile, is a complete mystery.

Out of Universe discussion

Essentially, the Shivans as of 2367 view humanity and the Vasudans as an "it", a cancer-like space growth encroaching on what Shivans believe to be their turf (our galaxy) and threatening their existence (as the Shivans are incredibly paranoid). They see no more evil in slaughtering Terrans and Vasudans than a Terran does in killing rats or taking antibiotics. Other creatures with subspace technology and weaponry are only thought of in terms of their potential to harm the Shivan species, not as people with their own minds, hopes, and dreams. The Capella incident happened because Admiral Bosch approaching and speaking to Shivans in their own language essentially shatters the worldview that Shivans have held for the last 30,000 years. It also, from the Shivans' point of view, completely changes the moral nature of the conflict: if Terrans and Vasudans are people instead of vermin, then what the Shivans have done in the past is an atrocity of unimaginable proportions.

I believe that the Shivans formed a giant subspace node to get as far away from Terran-Vasudan space as possible. The supporting fleet that followed the juggernauts into Capella was nothing more than a diversion to conceal the Shivans' true intentions and keep GTVA forces from getting near the juggernaut fleet. They were viewed as expendable and sacrificed so that the juggernauts could make the jump undisturbed. The destruction of Capella was just a necessary side-effect of the node formation (considering the way subspace nodes seem to be arranged and to function, it is unlikely the Shivans could have done this wherever they wanted. At any rate, the Shivans have, to put it lightly, a lot to think about, and if they come back, it will be in a very different role than as rampaging "Great Destroyers". It is not unlikely that the Shivan leadership, whatever it is, might fragment, perhaps with elements of the Shivan political/social unit denying what was learned from the encounter with Bosch and insistent on continuing the extermination campaign. If you want to look deeply into Volition's description of the Shivans as "a symptom of a bigger problem", the Aggressors could very well be that, especially if they have made any technological progress in the last 30,000 years.