I have issues with the entire plot of Mass Effect 3. While entertaining I seriously doubt any military commander would sacrifice his entire army for something they don't know how to use. Its completely ridiculous, any military commander with half a brain would've did something similar to Battlestar Gallactica. Evacuate and flee hoping to find somewhere else to live.
This is my suggestion on an entirely different plot;
1. The story begins much the same as current. John Shepard flees earth hoping to gather friendly forces in the hopes they together might stand a chance of fighting the Reapers instead of being picked off one at a time.
2. Priority : Deep Space Recon Station
Your intel reports indicate Cerberus is looking for a relatively secret Space Station that was intended to probe dark space. When you arrive you find Cerberus forces but for the most part the station is empty. When you arrive at the final room you find some intel which indicates a ship arrived recently from Dark Space and this is what Cerberus is after.
3. You begin to hear the illusive man speaking & appearing to you in dreams. You learn from Kelly Chambers that Cerberus did indeed have a control ship implanted but she doesn't think they'll ever use it. You begin to get very suspicious about these visions and dreams. Also your team begins to grow suspicious of your odd behaviour and they all act distant.
4. Priority : Alliance Base
Intel reports indicate the vessel from Dark Space which appears Reaper in origin has landed at an Alliance Base. Cerberus has launched a small fleet to try and capture the vessel & anything of use. You arrive with your team and begin to work through whats left of the base. You come across dead Cerberus & Alliance troops.
After a certain point you start to confront Alliance & Cerberus fighting. Strangely the Alliance troops are attacking you but the Cerberus are not.
You can attack whomever you wish at this point to reach your objective. The command center.
Once you arrive the doors open & standing before you is John Shepard.
Suddenly the illusive mans voice starts to command you to kill him. You fall down and try to fight it but end up reaching for your gun. Suddenly you're knocked down from behind... by your own team member.
The other John Shepard walks up and tells the illusive man to show himself.
He appears and says that what he did was for the best. That you were just a clone of Shepard. The real shepard never died they merely made it look that way. For his last deed the Illusive man activates a control which makes the clone of Shepard dissolve.
The real shepard explains to his team what happened.
That he went on a covert mission to Dark Space to investigate the Reapers point of origin. To learn anything of use to help in the war. Shepard concludes by saying his mission was a success.
To be cont.