In the universe of the Mass Effect games, humanity is a young but formidable race having only recently joined a much larger interstellar community of aliens - led by a Council in an artificial 'world' known as the Citadel. The technology of the galaxy revolves around the generation and manipulation of 'mass effect fields' (gravity, dark energy), for numerous purposes - in particular space travel. In this universe, all life in the galaxy has been subject to a cycle of annihilation - 'reaping', so to speak - by a race of ancient, sentient and malevolent machines that cull all advanced societies every 50,000 years.
In this case, Shepard enters MCM from a vague point in between the games 'Mass Effect: 2' and early 'Mass Effect: 3'. The Collectors are defeated, yet the war against the Reapers and their allies continues.