Silent Eyes was supposed to be in fact a huge interlude, a story that would fill in the missing parts in SG1's storyline, deepen Cerberus as an organization as well as the post-Capella GTVA. Our protagonist (I can't remember his name) is an SOC operative who defects and joins Cerberus while in secret he remains loyal to the GTVA. He wears an organic chip within his brain that would use quantum entanglement to undetectably report his progress to his direct superior - Captain Snipes. Our hero gets promoted higher and higher within Cerberus ranks to find out the organization's plan, why they cut off the Wolf's Group and most importantly - to locate the third Cerberus leader, the Phantom. In our missions for Cerberus we would meet numerous groups of interests, mercenary groups, gangs and our old friend dr Mina Hargroove who now owns a large corporation and cooperates with Cerberus. Our main antagonist would be Admiral Sain - a ruthless GTVA commander known from the SG1 prolog who now leads his own crusade against Cerberus for killing his son, colliding with SOC plans to infiltrate the organization.
Piece by piece we uncover what's going on in Cerberus - about the mysterious species they planned to use both to overtake the GTVA and defeat the Shivans. Kaimler Ovadiah was responsible for finding the Nightmares and waiting until Phantom finds the Shivans, but he betrayed the rest of Cerberus by cutting off the Wolf's Group. Phantom (Bosch) was also playing his own game - he wasn't going to defeat the Shivans using the Nightmares, but to open the way for his return to the GTVA and use ETAK to form his beloved Terran-Shivan alliance.
Final missions take place in new Vasudan colonies beyond Altair where we locate the second Shivan Gate. We fight Vasudan colonial militias, mercenaries and later GTVA reinforcements too. When Phantom's ship (at this moment we still think he is on board) finally shows up to open the portal, we reveal ourselves and together with SOC we try to capture him, but we are betrayed by one of ours, SOC forces are defeated and Cerberus opens the Shivan Gate, Shivans start pouring into GTVA space. In final mission we join forces with GTVA reinforcements and attempt to re-capture and close the portal (Andante-style) but we fail and Shivan invasion begins.
Later, in SG3, as Grizzly we join forces with Snipes and our Silent Eyes' protagonist and attempt to capture Phantom once again - he is then revealed to be Bosch and that we was not in the GTVA before the Shivan invasion and all our attempts from Silent Eyes were for nothing.
Who did that mystery ship discovered beyond Spica belong to?
It was a destroyer of Glantedoross Enclave, a post-Terran faction formed by Capellan refugees who found the Nightmares earlier. They were somehow altered by the Nightmares too, but I can't remember the details. Anyway when Adrealon was destroyed by the Wolf's Fleet and Ovadiah took over the Nightmare armada, the Enclave went into hiding. As Miles we return to Nightmare space with SOC task force and attempt to wake up the other Hivens who would take the armada back from Ovadiah's control and help us fight the Shivans. Glantedoross reveals themselves then and helps us.