Welcome to Reaping the Storm, the sequel to The First Human Spectre, set in the aftermath of Shepard's death. For those of you who already have read TFHS, yes, I know you're all eager to see how ME 2 will play out, but we're not quite there yet. This story is meant to show the aftermath of Shepard's death and all the unrest he has created in the Alliance. Different to The First Human Spectre, it will be told in multiple PoVs, most of them only used once. Don't worry, it will probably be only about six or seven chapters before moving on to ME 2, only a loose series of events telling how people deal with Shepard's death and how the political fallout is.
For those who have not yet read The First Human Spectre: Naturally, I highly recommend reading it first, as it has greatly altered some of the canon outcomes of ME 1; parts of the story might not make any sense otherwise. However, if you don't want to prowl through 320,000 words, then you can read a summary here. Which might be generally useful for everybody, anyway.
So, The First Human Spectre's ME 1:
Shepard's Background: Earthborn, War Hero (past relationship to Sole Survivor)
Shepard's status at his death: Council Spectre; left the Alliance in protest over BAaT, no longer Commander, actively refuses that address.
Love Interest: Tali
Feros: Colony is alive, ExoGeni has withdrawn from the planet and will most likely soon go under.
Rachni Queen: Alive (and the Council is left in the dark about that or the rachni presence on Noveria in general)
Virmire Survivor: Ashley (has resigned from the Alliance Navy in protest over Udina's schemes for galactic domination after the Battle of the Citadel)
Wrex: Is alive (and Shepard has the cure for the Genophage, and will hand it to him as soon as he can pacify Tuchanka)
Human Councillor: Anita Goyle (has promised to uphold pressure on the Alliance on various matters)
Further Notes: Ongoing Council crackdown on Cerberus in process. Navigator Pressly is still alive as he left the Normandy after the Battle of the Citadel. Emily Wong and Kirrahe are dead. 'Father' Kyle is free and his group intact, hidden from the Alliance.
Not quite the usual ME 1 summary, is it? There's a more en detail summary of what changed compares to canon below. But first, I need to explain some stuff:
As you may have noticed by now, I try to stay close to canon, with the only changes being what Shepard did and how people react to that. However, there is one exception to that I should already mention: ME 3 canon will be generally ignored. The game was a catastrophe, and while everybody laments the ending, this really is the least of its problems. By far. So, should I ever get to ME 3, its entire story will have to be rewritten. However, this means ME 3 canon will also be ignored in matters already appearing before ME 3: E.g., what's on Kasumi's greybox, Cerberus' background, the details of the Geth War, the territorial extension of various races (it makes no sense that human space should be that large while species that have been in space for a thousand years only have so few colonies) and so on. ME 1, ME 2 and Karpshyn's novels are canon in regards to this fic, everything afterward can die in a fire.
This also extends to how Tali looks. The usage of a poorly photoshopped free stock photo was bad enough, but most of all I don't like how human it makes quarians. That's silly. Asari are supposed to be the most human-like species; that's kind of their shtick. Also I like if humans have one unique physical feature (i.e., hair), instead of all other races being derivatives of humans in one form or another, making humans for unexplained reason the golden mean. There were some descriptions of Tali without suit in The First Human Spectre, and I'll keep to that instead of ME 3 canon. Not that this will be terribly important in this story, but hey, once ME 2 comes up...
And speaking of Cerberus: You might notice I already gave this Shepard a strong hatred for that group even before ME 3 came out. So any opposition to Cerberus is not "Hah! Shepard won't let himself be fooled by those who'll eventually sell out humanity" or anything like that. Rather, it's all based on how they're already presented in ME 1/2, the atrocities they've done there. In fact, I'm annoyed how they're enemies in ME 3. I'd rather have liked the opportunity to attack them first... So I'll even spell it out already here: Cerberus will not be indoctrinated, and never be in any way on the side of or be associated with the Reapers. And never suddenly grow into a mega-army, either. Basically, it will always be ME 2 Cerberus, fighting for humanity... or so they claim. Shepard won't be too convinced.
Oh, and while I have your attention, one more thing: Now, I can understand that some people got kinda annoyed how all the politics stuff took over a big part of the plotline in The First Human Spectre. That's okay and maybe I did overdo it. However, what I find kinda disturbing is people who do try to justify the Alliance and what they did. The thing is, yes, it's all just fictional stuff - but opinions about that do reflect back on people and their attitudes. And seeing some of those opinions, that can be a depressing thought.
Well, I just wanted to have said that. Now, let us take a closer look at just what has changed compared to canon in The First Human Spectre:
Not much to summarize, really. Go read The First Human Spectre if you want to find out more... Though basically, Tali takes over the 'LI role' in all aspects: The one bursting out at Liara after Therum, the one talking to Shepard after the lockdown, the pre-Ilos scene, etc. And seeing how an unusual Shepard this story's one is, this also has its affect on her: At the end of the story, she probably is slightly more willing to confront authority than at the beginning...
Shepard has Jeong and Dr Ross arrested, and gathers evidence for ExoGeni's crime: Abusing the population of Zhu's Hope as test group to see the effects of the Thorian, and then trying to kill them all, hundreds of people, to cover this up. Despite harsh resistance from the Alliance (who fears for ExoGeni's keystone role in its space colonization program) and the problems with megacorporate media, Shepard manages to publish his evidence with the help of Emily Wong and Anita Goyle (Udina's predecessor as Citadel ambassador, from the novel Ascension). In the ensuing trial, ExoGeni uses every trick to delay the process, but at the end of ME 1 its demise seems inevitable - either due to the trial or due to the horrible PR. However, this does not happen without casualties: Emily Wong is later assassinated while meeting with Shepard at Flux, and Tali is heavily injured.
Shepard's then girlfriend Sarah Schäfer committed suicide five years before ME 1 because she was this universe's sole survivor of Akuze and could not cope with the incident. Thus, when Shepard learns about Cerberus' role in this he swears revenge, especially since at time he already knows Cerberus is also responsible for the dead marine platoon on Edolus and the eradicated pioneer settlement on Chasca, too. Using Admiral Kahoku's data, he attacks the Cerberus bases on Binthu and Nepheron - and tells what he has found to the Council. The Council is utterly shocked about the finding of live rachni, an enemy they had thought long dead, and hence does everything to come cracking down on Cerberus.
Shepard also sends the encrypted Cerberus data found on Nepheron not only to the Alliance and the Shadow Broker, but to every intelligence service in the galaxy, hoping to hasten Cerberus' demise that way. The revelations about Cerberus hurt the Alliance's image, since they have proven unable so far to reign them in, especially as later Shepard fully publishes his findings (except the rachni) in asari media, but the Spectre does not care much about this. Furthermore, he does not tell the Council about the rachni queen on Noveria, since he frees her and has no intention to broadcast that. Hence, the Council is left wondering about the origin of Cerberus' rachni, and thus upholds the crackdown, which at the end of TFHS is still ongoing. Also, Cerberus' existence and crimes are public knowledge by the end of TFHS due to Shepard (see below).
When Shepard learns about BAaT from Kaidan, he reacts with an angry condemnation and says if this had happened to him, he would have joined one of the biotic terrorist cells. He is angry about this Alliance atrocity, and angry it appears like the Alliance has gotten away with it. However, a sequence of events he gets into changes that: During his mission to Major Kyle, one of Kyle's followers, Tisiphone (a non-believer of his cult of personality, who is only there because it gives biotics a community and sense of belonging) shows Shepard some victims of BAaT, who tell their stories to the Spectre. He is deeply disturbed by the injustices done to them and their ongoing marginalization, especially as it is something that could have happened to him had his biotic potential be discovered earlier. Thus not only does he not arrest Kyle (as that would destroy the group, robbing these desperate people of the only thing they have), but he also decides to give a new hide-out to his group in one of the bases he cleared of criminal elements earlier.
Grateful, Tisiphone informs him of the planned hostage taking of Burns, Chairman of the Alliance Parliament Subcommittee on Transhuman Studies, the man responsible for biotic affairs and for further denying reparations to the L2s. Shepard arrives at the hostage scene, where he is received peacefully due to Tisiphone vouching for him - and arrests Burns for obstruction of justice, as he has taken part in the classification of BAaT data. He gets Burns to give him all relevant data by threatening to fly him into a combat zone, and leaks those to asari media contacts given to him by Emily Wong. This causes a huge uproar in the Alliance. Most people condemn Shepard for the revelation of the crimes, rather than the Alliance for the crimes, but there is also much protest and outrage among humanity. More importantly, the asari condemn the crimes, and the turians join in for no other reason as to diplomatically harass the Alliance, so the Council begins to apply pressure on the Alliance over the matter.
Anita Goyle takes over both the legal battle against ExoGeni and the battle for justice of the BAaT survivors. At the end of ME 1, this battle is still ongoing: A deep divide runs through human society, and Council pressure on the Alliance is ongoing despite now being human-led (see below). Also, the Ascension Project is falling down hard: Most parents have recalled their children, as they do not trust the Alliance anymore, most enrolments for the next years have been cancelled, and the facilities are occupied by protesting instructors (some of them themselves BAaT survivors) and some of the older students.
Virmire and the Genophage
Upon arriving on Virmire, Shepard's first instinct is to simply bomb away Saren's facility from orbit. However, he changes his mind when he hears that Saren has a cure for the genophage, and instead simply agrees with Kirrahe's plan. As this plan has him infiltrating the base, far away from the salarians, that gives him the opportunity to grab the cure and keep it secret from the STG. With the aid of Rana Thanopti's codes Tali can download all necessary data. Nonetheless, Rana is shot as a potential witness and for her crimes against the imprisoned salarians.
Shepard successfully managed to keep his possession of the cure a secret. He promises Wrex that he will give it to him, as soon doing so will not risk immediately starting another round of the Krogan Rebellions, i.e. as soon as his race has settled down a bit.
Shepard's and Ashley's relationship to the Alliance
Due to his arrest of Burns and the leaking of classified Alliance data to the asari, Shepard gets a nasty surprise when returning to the Citadel after Virmire: The Normandy is grounded, Shepard recalled as her CO, and suspended from the Navy. Enraged, Shepard calls it quit on his part, and throws his Star of Terra and rank insignia to Udina's feet. With Anderson's help, he takes over the Normandy and flees the Citadel. Since then, he does not wear the uniform or any Alliance insignia anymore at all, and also rejects being addressed as 'Commander' - he has completely broken with the Alliance. As a "parting gift" to the Alliance he leaks to his contacts in asari media how the Alliance had tried to suppress the ExoGeni trial, how it done forbidden AI experiments on Luna and the existence of Cerberus.
While mutineers, the Normandy crew saves Terra Nova from batarian terrorists (Bring Down The Sky DLC), something that causes great embarrassment to the Alliance - they had not been able to protect their largest colony, and instead mutineers had to do it. Additionally, Shepard uses the spotlight and rewon hero status for a grand public speech where he condemns en detail the failings and atrocities of the Alliance.
Ashley, meanwhile, is very opposed to Shepard's course, but can also understand him and admits he is only telling the truth. Still, her loyalty to the Alliance holds, resulting in many heated arguments with the Spectre - until the Battle of the Citadel. Shepard decides that that Fifth Fleet should concentrate its firepower on Sovereign, since he has no idea whether they can stand against both the Reaper and the geth, and would rather not risk it: Sovereign must be defeated at all costs. Thus, ironically after everything, Shepard hands the Citadel to the Alliance on a silver plate. Udina wants to establish sole human domination in the galaxy - but to Ashley, that merely confirms that whatever Shepard has said about the Alliance is true, that they are still willing to sacrifice everybody to gain power. Thus she tells the ambassador she is leaving the Alliance, too.
The New Council
Despite Udina's initial schemes, In the end, Anderson and Hackett can convince him that establishing a new, human-led Council is the better alternative. Shepard nominates Anita Goyle as Human councillor - a valid choice, as she was Udina's predecessor and hence has the necessary experience. And since Shepard's heroism is the only legitimization for the Alliance's restructuring of the Council, the Alliance has little choice than to accept her. At the end of ME 1, she promises to continue the fight for the BAaT survivors and the survivors of Zhu's Hope, if need be also against the Alliance despite being the Alliance's councillor.