So I just completed the Heir to the Empire trilogy by Timothy Zahn. According to the Star Wars novels timeline at the back, if you skip the X-Wing book, it's the Jedi Academy trilogy next.
So I bought Jedi Search and started reading. But here I start reading about an imperial civil war, Luke being turned by a resurrected emperor and Han and Leia's three children.
Now, this is not where Last Command left me. So I reckon there has to be some books (or book) in between the trilogies (excluding the X-Wing book, because I checked, and that one was written after this trilogy.)
Anyone that can help?
What you are looking for is the Dark Horse Comic Series "Dark Empire" (& "Crimson Empire" as an extension), which depicts the events after the Thrawn Crisis and involves the "Resurrection" of Palpatine and the last major Clash between the Galactic Empire and the New Republic, well the final one of great scale at least. You can read the summaries on http://starwars.wikia.com
since the comics aren't that easy to get anymore.