What follows is a brief prologue to the following AU of Mass Effect 3, just to clear up a few points and because I can't resist writing up headcanon.
Following the events of the Suicide Mission, the Collector base was saved but Shepard passed as much information about the Collectors, and the way through the Omega-4 Relay, to the Council rather than surrendering it to Cerberus. After several clashes with Council reconnaissance forces, Cerberus conducted a large raid through the relay, taking the remnants of the proto-Reaper from the Collector Base and disappearing, maintaining an ominous silence ever since.
Shepard cut all ties with Cerberus and, through Councillor Udina's machinations and in recognition of the Collector intel Shepard had acquired, Shepard's Spectre status was officially upheld. Her rank of Staff Commander was reinstated but she is currently on permanent secondment to the Spectre Office.
The Normandy SR-2, despite heavy damage during the Suicide Mission and losses amongst the crew, is re-fitted and remains under Shepard's command as "an independent Spectre vessel". After a full refit (funded from Shepard's previously unknown personal resources) Normandy is frequently seen heading between the homeworlds of all Citadel races with long sojourns in the Terminus.
Doctor Liara T'Soni, as Deputy to the Shadow Broker, established an operations and communications room in the former armoury on the CIC deck.
One Lieutenant James Vega of the Alliance Marine Corps, rescued by Shepard and Garrus Vakarian from a bar brawl on Omega, is attached to the Normandy as an Alliance Military Observer and replaced deceased Jacob Taylor as Armoury Chief and head of the marine detachment.
Chief Engineer Tali'Zorah vas Normandy returned to the Flotilla to delay any moves towards war with the Geth. At Shepard's request, the Alliance transferred Lieutenant Greg Adams to the engineering crew of Normandy as a Technical Observer.
Gunnery Officer Garrus Vakarian, left the Normandy to take up a position as Special Operations Advisor the Primarch of Palaven.
Miranda Lawson, after providing the Spectre Office and Alliance Intelligence, is released on Commander Shepard's authority and resumed her duties as Normandy's Executive Officer. Her release, and service aboard the Normandy, is not widely known outside of the Council and Alliance High Command.
The sacrifices made by Jacob Taylor, Zaeed Massani and Justicar Samara, ands those who died during the service the Normandy SR-1 are recognised on the SR-2's memorial wall located on the crew deck.
In the six months between the Normandy's assault on the Collector Base and the beginning of the Reaper War, there was a catastrophic disaster deep within Batarian space when the Alpha Relay mysteriously exploded and took the Bahak system with it. Although the events around the annihilation of Bahak remain shrouded in mystery, The Batarian Hegemony made accusations about Alliance interference in the system prior to the relay's explosion and that a vessel bearing a strong similarity to the Normandy was recorded by Hegemony surveillance stations heading through Batarian space at the same time. Commander Shepard denied any involvement with the Bahak disaster but voluntarily submitted herself before an joint Council-Alliance investigation on Earth in 2186.