It takes place about 120 years after the battle of Yavin. The Empire in this story is not the evil faction, I'd say they are a grey faction, with the Jedi as light and Sith as dark. The Alliance of free planets are wiped out and absorbed into the Empire. The war seemed to have started over misunderstandings and political necessity rather than ideology. After the Alliance are defeated, Emperor Ronan Fel asks the Jedi to lay down their arms and swear allegience to the Empire. Some do, becoming Imperial Knights, but many refuse, gathering at the planet of Ossus. A few days later Sith and Imperial forces attack, and the Jedi are more or less wiped out except for a few that manages to get away.
A short time after the Massacre at Ossus Darth Krayt, leader of the Sith faction, marches into the throne room and cuts down the man sitting on the throne, proclaiming himself Emperor (that's what you see in one of the pictures). But it turns out he just cut down a stand in, the real Emperor was still alive, in hiding, gathering loyal forces to him, eventually retaking Bastion. So the Sith sits on Coruscant, the Emperor on Bastion, starting eachother down.
A great story so far. I don't care to much for the main character or the people around him, but the Imperial and Sith factions are really cool, and their civil war with stormtrooper against stormtrooper are very interesting.