Han gets captured and enslaved on kessel. He meets Kip Durron and they help each other escape, but into a Maw of a forming Black Hole. Luke is trying to find Jedi for his academy, but a Dark Force spirit is threatening the students. In the finale, the student must fight the "ghost". This trilogy when combined with I, Jedi are important contributions to the SW Universe. We get Kessel, the Maw installation, Kip, adm Daala who reappears then disappears, Qui Xu, the first hint of the aftermath of Dark Empire, and more Wedge (now a critical character).
I had some problem with the story like: The spirit of a dead jedi having such tremedous power, the whole idea of the Suncrusher and the studip diversion of the blob race storyline. Unlike some, I feel that some of the darkhorse comics have made important contributions the SW Expanded Universe. Dark Empire was one of them.
For those of you who plan to read the New Jedi Order books, you'll find that Kevin J Anderson has made important contributions to SW including this trilogy and the young jedi books (the YJ books are surprisingly good).