The SC Thanatos was in the last mission of FS2 Main Campaign, and was a Rakshasa-class cruiser. It was brutally slaughtered by the GTCv Lemnos, the GVC Ptah-Nu, and the 70th Blue Lions elite squadron.
As for the big disappearing fleet (consisting of 20-ish Fenrises, 9 Reliants, and 3 Orions), that was one of the main plot points of the FS1 campaign "Awakenings". Only one of the Fenrises (the GTC Hornbeck IIRC) made the jump from Antares to Vasuda successfully.
Two of the Orions (GTD Iowa and GTD Moscow) randomly appeared in Vasuda in 2338 (a 10-year delay), with no crew on board, and were subsequently refitted. Nothing is known of the other ships.
Of course, none of that is canon, but I've always been fond of Awakenings. It was the first campaign for FS1 that I really considered "good", besides the main campaign. And it was the first campaign that established the GTD Reliant class as the one preceding the Orion.