Clear Skies/WMG

Clear Skies and her crew returned from Jovian space not long after the end of Clear Skies 3.

We know that they won't be taking apart Clear Skies, and they also have the decency not to kill J.R. just to get their tech out of him. So their plans involve both remaining intact.

Now, if you were the Jovians, what would you do with a Minmatar battleship that has been upgraded with Jovian tech? I can't think of anything that Clear Skies could do in Jovian space that a Jovian ship couldn't do better. In fact, there is only one advantage that Clear Skies has over Jovian ships: it can run around non-Jovian space without drawing much notice. On top of that, the ship's crew have shown themselves to be competent and reliable, once they've been convinced to do a given job.

The obvious answer, then, is to send them back into the rest of the universe as your agents, perhaps after upgrading Clear Skies further to give it a major edge against any subcapital it fights. Heck, it might even make sense for Smith to use Clear Skies as his command ship.