As i've seen JK and JC stories and we all know how the game will end, the Imperial will lose and the Emperor will die, so as stories wise goes, i would say the JC would be sent to investigate the ritual that the Emperor will use which i think will meet the SI, they may have to join hand to stop the ritual .While the JK will confront the emperor and the SW. I would say the ending will be the SI will escape while the others of the Dark Councils will be dead - well may be because of SW is sent to kill them for their treachery acts, or the SI and the JC kill them cause they well in the way of preventing the ritual - The SW i guess will be dead cause he is Lord Wrath, if the Knight want to kill the Emperor he need to kill Wrath.
The trooper and smuggler may join hand in attacking Imperial strong hold while the agent is sent to sabotage their bases.
not essentially the Wrath will die because Scourge was the Wrath and he still ended up betraying the Emperor. Perhaps the Wrath will have to make a huge decision wether to bring down the Emperor or not, and eventually all of the classes will be united together standing against the Emperor