Since Mass Effect 2 is supposed to be better than the first somehow, I've done a little thinking, and this is my guess as to what the plot will/could/should be like;
Sheppard was forced into reclusion by the religious groups and tabloids that ridicule and scandalize her relationship with Liara. When Liara became pregnant, the couple decide to flee on the Normandy to live in a distant, more open-minded colony. On the way, the gang is bombarded with asteroids that Joker claimed to have not been on the map and/or did not exist at all and/or no other pilot could avoid as valiantly as he, the greatest pilot in all the yadda yadda. Their ship, a husk of its former beauty, spiraled through space and ends up desintegrating in the atmosphere of Kahje, the homeworld of the Hanar. Sheppard, dead, drifts through the gigantic ocean until she reaches a very, very polite colony of Hanar, who resurrect her and worship her as a god. There, she must find a way to request a transport off of their god-awful world, but as to not offend them or imply that their hospitality was somewhat unsatisfactory.
Once off of Kahje, Sheppard must take the phoenix mirror and ask around the Citadel for where she can find Lan Di, as well as find a part-time job. One night, after her watch tells her to go to a hotel and sleep, she is visited but the Daedric god Azura, who tells her that she is the Nerevarine and that Lan Di is actually none other than Dagoth Ur. She is sent to Skyrim where she must fulfill some prophesies, as they were written in the Bethesda newsletter as "So, yeah, ES5 will probably might be Skyrim since we trademarked the word, blah blah about other games." Completely bypassing the third and fourth installments in that series, she orders Carth to pilot the Siltstrider to Taris, where they can be blown to shit by Darth Malak in a spaceship that isn't the Death Star, escape with Bastila alive, destroy Dagoth Di using the dragon mirror and the now-fully-explained floating sword (named "Keening"), resurrect some Dwemer/Protheans/Quin Dynasty to find out just what the hell they were, and dramatically fly away from a big explosion in the Ebon Hawk. The end of the game would be the characters landing on Earth in the player's hometown to havoc on their enemies' shrubbery and the like until they pass out from all the FUN.
I think a game like that would satisfy absolutely everybody's needs everywhere so that they can all shut up.