It's fine. I've got something figured out, and was probably gonna post it no matter what.
So far what I've got is that Cerberus dissolved after the Reaper Crisis, but some of its assets were maintained by Miranda Lawson. These included samples of Collector DNA. She brings on Javik, last surviving Prothean, to a project that was, essentially, designed to recreate the Prothean race. The science behind it, as far as I can come up with, involved cloning the Collectors, but altering them on a genetic level to be more similar to Javik's, with some alterations for male and female. The new organism would be, on a genetic level, "cured" of their originator's extensive indoctrination and genetic modification. (this process is where suspension of disbelief really comes in handy) Following the species resurrection, they swiftly grew out of control of the Cerberus remnant, and finally the Council itself. Using their inherent genetic superiority, growing numbers, and access to ancient Prothean tech scattered across the galaxy, utilized as infrastructure by many races. The rise of the Protheans led to the establishment of a new Prothean Empire on the fringes of Citadel space, gathering other races under their banner (the Hanar, who believe the Protheans to be gods, and the Drell who owe allegiance to the Hanar; the Yahg, who were conquered and dominated by the Protheans; the Batarians, who sought to spite humanity and the Citadel; and the Volus, who were exceedingly frustrated with their lack of progression under the Council). After a brief war that neither side could win (the Council's well-armed and well-trained army balanced against the highly-advanced and genetically superior Protheans), the Council and Prothean Empire came to a tense peace, and galactic relations returned to a relatively normal state.
However, as the Prothean Empire grows in strength and prestige, the Council grows impatient with the Protheans' refusal to adhere to the current galactic status quo. In order to facilitate the fall of the Protheans, remove an enemy power, and reassimilate the Hanar, Drell, and Volus, as well as obtain the Protheans and Yahg as new members, the Council orders a task force of Spectres to travel through Prothean space, eliminate their hierarchy, sabotage their infrastructure, and deliver information and technology to the Council.
The setting is a few decades after the events of ME3. Shepard's dead (fuck the extended ending), and we're going under the assumption that most of his crew members survived (or at least, as many as possible). The Spectres in question could be drawn from virtually any Citadel race (obviously Prothean and Yahg are exceptions. Elcor as well are undesirable because... Elcor). All of them have prior military, espionage, or covert operations experience (this extends to thieves, criminals, and mercenaries who are of an exceptional disposition), or are extremely special cases (i.e. a Jack of this present). The Council has expanded, creating seats for the Krogans, Quarians/Geth, and Elcor. The Krogans have expanded under controlled conditions, and have strict birth restrictions. They have "uplifted" the Vorcha in a similar manner to how the Salarians did the Krogan, using them as grunt troops to supplement their mainline military (they treat the Vorcha comparatively better than the Salarians did the Krogan). The Quarians currently live in symbiosis with the Geth: Individual Quarians are each paired at birth with a new Geth intelligence, which acts as a guide and companion to the Quarian, developing into new platforms as it grows. The two grow off of one another, and ultimately become a team in everything they do. The greatest sign of their synergy is how the Quarians and Geth have begun to meld into one individual, creating a Master Chief/Cortana relationship. Originally meant to cure the Quarians of their immune deficiency by creating incrementally septic artificial environments within the Quarians' clean suits, the possibilities of having an AI within one's head quickly became apparent. More can be added as the OOC is constructed.
Anything sound good here?