SPOILERS

A little bit after hitting tech 5 there will be a mission prompt to take Obi-Wan to Utapau. Then you will fight a tactical land battle (after clearing space above) using only Obi-Wan and you need to kill Grievious. It is a pretty hard mission because Grievous does so much damage.

Once you complete that and a little time has passed you get prompted to take Anakin and Palpatine to Coruscant. If they are already there, manually take them to space and then re-place on ground. They will disappear. You will see some story stuff and then Order 66 happens, Jedi hero units disappear and you get Emperor Palpatine (useable in land combat), Vader in-suit, Tarkin,and a few extra Star Destroyers.

That is the end of the story stuff, as best as I could tell. No mission to Mustafar, at least that I encountered.

I THINK after the Grevious mission he is dead for good, I didn't notice him respawning anyway. Makes it weird to see Dooku after the mission because he respawns... I may make a copy of this mod on my local harddrive and turn perma-death heroes on. :)