I could be mistaken here, but I'm pretty sure that in the first Darth Bane book he pretty muchs wipes out all of the Sith. I mean, he does in fact wipe them out, but I don't know how the timeline from this game ties to that timeline.

The game starts in 3643-3641 BBY. Desoulous birth is given as ~ 3522 BBY. He's a master when he falls, so probably no earlier than about 3480 BBY. There could still be a Sith Empire of some sort existing then, his story doesn't rule that out.

Darth Phobos is placed usually between Darth Desolous and Darth Ruin. She was killed by a combined group of Jedi and Sith. Her placement is vague, though.

Darth Ruin, originally Jedi Master Phanios, ends an apparently long era of peace when he falls to the Dark Side in about 2000 BBY and establishes a New Sith Empire with 50 Jedi Knights. It's not a total re-establishment of the Sith, though, as there are still Sith Cults existing that he joins under his banner. But organized Sith of the higher level seem to have been long gone by then.

Darth Bane betrays Kaan's Brotherhood in 1000 BBY, bringing an end to the New Sith Wars that Darth Ruin started.