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Okay some of the smaller stuff aside this was my idea of how to take what Bioware has given us and tweak it just a little to satisfy my expectations for the game.
So fast forward to Shepard coming face to face with the catalyst. The catalyst resembles the Reapers that have come to Earth (maybe resembling Harbinger) He uses the same basic argument about synthetics and organics and harvesting organics to preserve them. At this point Shepard argues that that might have been true in the catalyst's cycle but here and no synthetics and organics are living, working and thriving together. Catalyst finds this hard to believe but the fact that Shepard has made it this far means that he is no longer able to do his job effectively so Shepard is given a choice.
Choice 1: Control (Catalyst makes a damning argument about how Shepard will regret destroying them when the cycle repeats itself) Shepard can control the Reapers. Shepard dies. We see the Harbinger hologram be replaced by one that now resembles Shepard. Shepard watches as the Reapers leave Earth then the Shepard hologram flashes off.
Choice 2: Combine (make a new race of synthetic/organics) This would guarantee Shepard lives. There is a flash of light and Shepard wakes up on the battlefield. Depending on the Galactic readiness the level of destruction and number of surviving crew will vary.
Choice 3: Destroy This action destroys the catalyst and as a result the reapers. This should not prove exactly easy but take into consideration that Shepard is injured so it shouldn't be impossible. With the catalyst and reapers destroyed Shepard collapses and again depending on Galactic readiness Shepard may or may not die. If the Galactic readiness is high enough someone (Joker) gets the Sheardp before they die.
In all 3 choices the Mass Effect relays are not effected. And after the choice is made, which ever it is we see a variation of the same epilogue: It is a short time down the road and there is a memorial in progress for those who died in the war. The same memorial is held on other planets at the same time (Earth, Palavan, Sur'Kesh, Thessia) there is a reading of names and signs of reconstruction. (If Shepard died their name is mentioned at every memorial.) As the zoom away from the ceremony on Earth in the back of the crowd is either Shepard alone, Shepard's love interest alone, or Shepard and their love interest arm and arm.