You've either destroyed the Reaper-making platform or delivered it to the Illusive Man. And...uh oh! Turns out you're expendable. He deactivates your Lazarus Project implants, which would have killed you but for the quick action of Dr. Chakwas (class-choosing and face-configurator time!). Not sure who is on what side anymore, you start trying to put together the mystery of who the Illusive Man is. And the truth is this: he's not the most vigorous defender of humanity against the Reapers. He's a false flag. The Reapers took over the mind of a two-bit anarchist/terrorist (ever wonder why his irises are made out of electronics? Same reason Saren got covered in cybernetics as the Reapers took him over) and made Cerberus what it is today. He was using you, not to defeat the Reapers, but to help recover a stolen Reaper platform from the Collectors/Protheans, who had broken free of their Reaper enslavement and were planning on using the Reaper-ship they were building to attack the Reapers with their own technology.
Without Cerberus backing, you're now just a rogue badass who is trying to convince the galaxy of a coming apocalypse. Although you're able to put together a team by the time the Reapers arrive, you haven't convinced anyone in the galaxy.
The Reapers hit hard. First Turian space. With a salvaged SR-1 Normandy, you and your loyalists fly out to try to help, but it's no good. Turian refugees flee to other areas of space, but most are lost under the bombardment of the Reapers...and more sinister, their widespread capture of civilians and conversion into husks, scions, and other fighting machines.
The council listens. They help complete the repairs of the SR-1 and even make it better. They give you some resources to back your mission. You're a respected, active-duty Spectre again.
Then the Reapers hit Salarian space. Despite other Council races pouring in some ships to help, the same thing happens that happened to the Turians.
Then the Asari. The Reapers are unstoppable. A battleship even bigger than the Destiny Ascension fails, and it appears all hope is lost. But then, you find something out. Before the Salarian homeworld was wiped out, some Salarians came up with the superweapon you are going to need to destroy the Reapers. The genophage cure. Come on, they've been hinting at this since ME1. It's the only way that the Rachni Wars were won (when the Rachni were the Reapers' first servants in Council space). And an army of husks is nothing to a charging Krogan phalanx. Only problem? The genophage cure is in an abandoned laboratory on the Salarian homeworld in Reaper-controlled space. Guess who has to go behind enemy lines to retrieve it?
So you get the genophage cure, drop it off on Tchuchanka, and then receive the distress call that the Reapers appear to be headed to human space next. The human fleet and human armies won't be able to hold them off for a few years while the genophage cure works and a new generation of Krogan warriors is born. So you need to gather unlikely allies. The Rachni. The Vorcha. The remains of the Protheans (who admit the horribleness of what they were doing on that platform, but thought it was the only way to stop the Reapers from killing everyone in the galaxy).
Cut to the teaser trailer. The Reapers have landed on earth, and the husks are spreading like a zombie outbreak. Every human who falls becomes another footsoldier for the Reapers. Humans don't know if they're going to hold out. Then you come riding in with your motley army of Rachni, Vorcha, and Collectors. A great battle ensues for many months. You push the Reapers off-planet. You fly to Mars. Another long, drawn-out campaign, and you push them off-planet there. But they redouble their efforts, and it turns out that the great battle for humanity will occur ship-to-ship, boarding-party-to-boarding-party, out in the asteroid belt.
And the battle is not going well. You're taking high casualties, because the Reapers can use their ships AND their husks in perfect conjunction in this battle. When it appears all hope is lost, though, the cavalry arrive. Thousands of troop transports carrying Krogan warriors jumps in. The reapers are destroyed.
The council is rebuilt, and two new seats are awarded to the collectors and the krogan. The species of the universe worries about future war between Krogan, but at least they're there to discuss it. There were always be wars, but there will no longer be complete obliteration every few thousand years. The Reaper's cycle has been broken once and for all. Curtain.