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Since I simply don't have that much time to sit and type for hours a theory as long as the Shivan Manifesto, here's an analogy of the Shivan agenda.
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The Shivans are the guardians of the universe. Whenever there's some sort of violent trouble in some system in the vast expansion of space, they come and start screwing things up for the better. For example, when the Ancients grew a literally MASSIVE empire (possibly thousands, or even million of systems but we don't have proof of that), other species gradually phased out and were crushed by the Ancients. So the Shivans organize a huge assault on the Ancients until they are wiped out. After all, the Terrans wouldn't be making sh** like Orions in the 24th century if the Ancients hadn't been wiped out earlier.
As noted in the wiki, it's possible that Volition wanted the supernova of the Crab nebula to have a part in the destruction of the Ancients. At some point, the Ancients were pushed back to this nebula and the Shivans blew it up, causing a subspace ripple (as stated in the cutscene) and dispersing the Shivan fleet (the Shivans dispersed intentionally).
I'll also note the Knossos here. The Knossos, as carefully analyzed by Terrans, was a tool utilized by the Ancients to stabilize a node on the verge of collapse. It's possible that, while the Shivans were pushing toward the center of the Ancients' empire (stated as somewher near Vasuda) the Ancients had undergone some fighting in subspace portals against warships that were probably similar to the Lucifer (only ships around the size of the Lucifer would produce explosions enough to severely damage subspace portals) and, while another Shivan fleet was nearing the node, the Ancients took some time to construct these gates, probably to send a fleet in to counter the Shivan shielded destroyers while in subspace.
Back to the major section. As the Shivans disperse their fleets, they tend to some business far, far from Terran space. And then, the Shivans intentionally SCARE the Terrans and Vasudans - by use of the Lucifer.
The Lucifer created a whole mess that soon united both Terrans and Vasudans. This was, actually, all part of the plan; the plan to trick Admiral Aken Bosch into telling him that "hey, it's all right. No need to start some messy rebellion when there's really no use in talking to us." Since then, the Shivans took hold of Bosch for perhaps the rest of his life - so as he won't reveal what information the Shivvies had inserted to him.
Now, why did the Shivans waste so much on the GTVA fleet? To tell them that there really was no use in creating a self-defence method against them - the Shivans weren't up to wiping out the Terrans and Vasudans (yet). They just wanted to slap the face of the GTVA in order to bring them back to sanity and maturity (since there was no use at all in fighting off the far more powerful Shivans).
Then the Shivans build some comm nodes to guide a large fleet they prepared to disperse AGAIN. The large fleet - well, you already probably guessed - the Sathanas fleet - had the capability to cause another star to go supernova, and cause a subspace ripple in which they could disperse in other parts of the universe as part of their purpose to restore order throughout the universe.
Also, we're not exactly sure of the identity of their masterinds (of if they had any at all). What I'm simply trying to imply here is that Shivans are God's rod which whips the careless, immature civilizations that quarrel among each other and discipline them.
Sounds like Shivans aren't bad guys here, eh??