^ This was suppose to take place after Shepard is done talking to Harbinger inside the Citadel. Their are few more lines, but they were not on the Disc. Shepard is inside the Citadel and His/her Squad is outside holding off the Reapers. Harbinger is set to wipe them all out and Joker arrives just in time to save everyone. Joker than goes head to head with Harbinger.
The Endings attached to these Scenarios are very different as well. I think everyone would have been happy with those Endings.