“Empire’s End” was the finale of the “Dark Empire” saga (Although it would have a sort of semi-spinoff with the “Crimson Empire” series). Although still written by Tom Veitch, the series only lasted two issues, and instead of Cam Kennedy doing the art chores (which gave the first two mini-series a distinct look), it instead passed to Jim Baikie.
In “Empire’s End”, the Rebels/New Republic is still on the run, with Palpatine still in a clone body. What’s worse, their new base is destroyed by the Galaxy Gun, although they are able to evacuate in time due to rooting out an Imperial spy and a defective Galaxy Gun missile.
However, there is still hope for the Empire’s defeat-Emperor Palpatine is dying, as his clone body is starting to age rapidly due to his dark-side use and having been poisioned. He’s pretty much run out of clone bodies and now seeks a new host-the infant Anakin Solo. (Yes, that’s right, the Emperor basically is Vigo from Ghostbusters II)
It pretty much all ends at Onderon, the beast-world from the “Tales of the Jedi” comics (and still in Disney canon thanks to Clone Wars). While Luke, Han, Leia and their small group of force-sensitives try to protect Anakin from Palpatine on the surface, while a rebel strike force takes on the Emperor’s Star Destroyer Eclipse II in space.
The ship is sent through hyperspace accidentally back to Byss, where it crashes into the Galaxy gun, which causes it to launch a missile and destroy the Imperial throneworld.
Meanwhile on Onderon, the Emperor tries to steal Anakin and posess him. Han shoots Palpatine in the back, killing him but unfortunately allowing his force spirit to make a leap for Anakin.
However, Empatojayos Brand-the Jedi with a floating cyborg body-intercepts the spirit, having him pretty much posess him instead (although Brand’s personality still maintains control). Brand then dies, taking the Emperor’s spirit with him forever.
This ends the “Dark Empire” saga, although Crimson Empire would pick up some of the plot threads (including what happened with the Emperor’s final clone, and what’s left of the Empire between this and the “Jedi Academy” trilogy). Luke, Han, and Leia’s adventures would continue in the Jedi Academy trilogy, although for the most part, major sagas featuring them post-“Return of the Jedi” were left to the novels for the remainder of the original expanded universe (Although there’d still be a few more novel adaptations and stuff featuring the heroes in their OT days).