- Project Lazarus: I would scrap this horrible Idea completely. Shepard falling into a planet's atmosphere would burn him/her up completely, only ashes would remain, and I'm being optimistic. I almost uninstalled this game right away wen I first played it because how stupid this hole thing sounded. The only reason this exist is because they wanted to tie Shepard to Cerberus completely.
- Instead of all that bullshit, I would build up the tension between Shepard (the player) and the Aliance/Council. The Collector attack would destroy the Normandy, kill most of the crew, but Shepard would escape in a pod with the surviors, critically injured and unconscious. Wen the pods land in the nearby planet, the collectors would send solders to pursue, but in that planet would have a secret shadow broker base. They would be saved by his army, lead by a young drell named Feron. But the whole thing was staged, as for a means the shadow broker could kidnap the unconscious Commander Shepard while they treated his/her injures. Events would unfold more or less the same, except that the rest of ME1's surviving cast would be there. In the end, Feron would betray the shadow broker, deliver Shepard to the crew and be captured. The crew would do the sane thing to do and NOT deliver Shepard into the hands of cerberus, since he/she would still be alive, but in a coma. Shepard then proceed to be treated in a hospital in the citadel, and would stay that way at least six months or so, and in the meantime, Wrex (if alive) would became leader of the urdnot clan, Tali would have to return to the flotila, Liara would became an information broker, the virmire survivor would be promoted and Garus would became archangel. If any of them were romancing Shepard, wen he awakes the doctors tell him that they had a very hard time leaving his/her side, but had to continue with their duties. But the always found a way to visit him and the hospital was sick of receiving their calls.
Immediately after being released, the news would spread that the "Hero of the Citadel" or "Human Supremacist" had finally awoken from his coma. Depending on witch the player is, people and aliens would salute him/her, or curse him, saying that he/she should have died, warm and fuzzy stuff like that 
After dealing with that, Shepard would be summoned to the council chambers and in this reunion would try to appeal to the surviving council or the new one to take more immediate action about the treat, but they would ignore like the asshats they are. Thus giving the player a choice
1)Continue on the spectre path: The player would have to work their diplomatic skills to get support to convince the council to sanction Shepard a new ship. This would be considerably harder if Shepard let the council die in ME1. Acquiring the ship, he/she could act with survivors from the collector attack that could answer to his call, and some new recruits. In this path, Miranda and Jacob obviously wouldn't be options, and the player would miss on their content. So, after talking to people in the Citadel and acquiring a new ship (and meeting Joker, he would be the pilot regardless of the scenario you choose), Liara and the Virmire survivor will arrive on the citadel, and will take Miranda and Jacob's place in the story.
Liara would explain the player that she is now an Information broker, and will use her connections to find suitable people for the mission, since most of the old crew would be unavailable. Her loyalty mission will be lair of the shadow broker of course lol
The Virmire survivor will join you for loyalty, and you already know their qualifications. Their function would depend on witch of the two you have.
+ Ashley would be responsible for the armory, like Jacob, and her loyalty mission would be saving the colony her sister lives.
+ Kaidan would be responsible about biotic amps and his upgrades for the ship. His upgrades would be about defense, and would develop a biotic shock absorver that would reduce biotic damage on the team. His loyalty mission would be rescuing his team of biotic students, and in the mission we would meet Rhana, the girl he talks about in ME1.
The ship would not have an AI in the start, but a recovered VI. Later the player will discover that the VI is the same he attacked on Luna base in ME1, but it was reprogrammed and repaired, and Its guarantied that its harmless. Of course, it will gain consciousness again, but this time, it will evolve into having EDI's personality, but will have other name of course. The final stage for it to gain consciousness will be the same as "unshackling" the original EDI. Personalities will be similar but different enough so it doesn't look like the same character.
The story will progress pretty much the same after this point, with some key changes:
+ The involvement of the player with Miranda and Jacob would be shorter, as they would not join the player's party, but they would still have a significative presence on this scenario. Player input would be crucial to their future in Cerberus. Miranda would be a Boss Fight at some point, but not die because of it. Their involvement could still be the same in ME3 (except for Jacob, I would definitely change that ¬¬), or they would be indoctrinated soldiers. Their romance act wouldn't be available of course, in their place, the player would have Liara and the Virmire Survivor.
+ In horizon the player would meet Jacob on a recon mission for Cerberus. The conversation would have a completely different tone than the one with the virmire survivor, but he will say he doesn't understand why Shepard still continues loyal to the Aliance and the Council. But he will say he admires him/her and hopes for the success of the mission.
+ Since Liara would be managing her business and an Information broker in the ship, she would find from one of her sources about the Collector base in the middle of the game. Turns out, her source was a Cerberus double agent, so the story could flow most the same, and the player would begin to formulate how him/her would handle Miranda and Jacob's situation.
+ The Illusive Man will still try to contact Shepard during the story and slip some information to him/her. He will say that even if Shepard mistrusts him, he wants him/her to succeed for humanity's sake. Shepard can say he/she is not fighting just for humanity.
+ The Council would be the ones that would inform Shepard about the direlict reaper.
2)Quit the spectre ranks and work with Cerberus: The reunion with the council would have to be particularly frustrating for the player for this to work. If it's the new council, it might make this decision easier on the player. Regardless of witch council the player has to deal with, Shepard will be denied of a new ship and the mission for support I spoke earlier would begin. The player would do this mission ALONE, as the surviving ME1 squad is not in the citadel at this point, the player already knows they are away in their business and would take sometime for them to arrive at the citadel.
During this mission, Shepard would meet Miranda and Jacob, and would present the alternative to the player: Work with Cerberus instead. Of course, they would present the player with all the best arguments possible, and if the player still says no, they would still be in the citadel for a while, in case Shepard changes his/her mind - they would be available until the player completes the mission for support, witch would lock the player in the spectre path.
If the player accepts, they would take the player to a secure place to talk with the Illusive man in a secure channel. This would be the last chance the player would have to reject Cerberus. If the player accepts, he/she would leave the citadel at once, and would, be considered kidnapped. After some time, the rumors of Shepard working with Cerberus would spread, and he/she would be branded a rouge spectre. The rest of the story would proceed more or less like in the actual game.
Like I said, Joker will follow you no matter the path you chose, but the ship you would get from Cerberus would NOT be Normandy SR2 (I like the ship too you know, but is too far fetched to have Cerberus build her, sorry ;/), but a newly designed ship made by Cerberus. EDI would not be the rogue Luna VI of course, since that would be the AI of the Aliance ship.
Other specters would come to hunt Shepard down, and Liara would refuse to see Shepard In Ilium at first, but after the missions you normally have to do there, She would agree to meet you and hear what you have to say, understand your reasons, but will not join you. The encounter with the Virmire survivor would be more or less the same in Horizon, but they would be even more angry at Shepard, as it was a conscious choice. Garrus and Tali would be meet in the same circumstances, the conversations would be a little different but Shepard would manage to convince them to join all the same.
Endgame: I know, the suicide mission is one of the best tings that happen in this game, but creates a handful of problems for ME3 ;/ I would move this mission concept for the end of the saga, and not make all the cast player determinant before the end of the story. The survival of some would still require player input, but at least 70% of the cast would be alive in the end. Unless you neglect the upgrades, that would cause everyone to die, including Shepard. But that scenario can't be imported to ME3, so it wouldn't be too much of an issue for the narrative. Regardless the scenario, the Illusive man would still contact Shepard and ask for him/her not to destroy the Collector base. The arguments he would use would vary greatly.
Side-quests: I would fire who thought planet scanning was a good idea (¬¬) and keep the system I suggested for ME1. I would recycle some planets I had in the first game (adding enough new stuff of course) and make new ones, expanding the universe.
Skill three: I hate the skill three in this game with a passion. Would have kept the one for the first game but given the player the option to have a more simplified one if they wanted.
Torna su
Remove any possibility of successfully curing the genophage (the reaper/thresher maw tangle could resurface just long enough to wreck the shroud at the last moment, to give one possibility).
