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Well the missions start after the original storyline end...... If you played the Vanilla version of Freelancer and finished it, you remember that you finish the last mission, and have nothing to do other than go to the bars, and do non-plot activities. Instead what happens is that the CF missions start off, and give you a few hours more of gameplay
As 50pack said, and that means:
If you load a savegame with the vanilla/original storyline already finished, the CF Extended part will NOT appear, as it gets engaged/starts in the moment you finish the last mission of the original story.
When activating the mod, the option you see there to "skip the storyline", it skips ALL of the story including the CF part, so don't try this, it's a waste of time.
You just have to load a savegame in middle of the original story, or near to it's end (like, before the last mission), and continue it. Or start it again and finish the original part 
