So basically the galaxy is under siege by an ancient race of sentient spaceship machines dubbed "the Reapers" that appear every 50,000 years to destroy, harvest, and re-purpose all advance civilizations to make way for younger, less advance races to grow and prosper. So after rallying the entire fucking galaxy to fight against this impending doom despite their own inter-species conflicts, finding the blueprints for an ancient weapon that has been continuously modified by species of past 50,000 year cycles and building the damn thing thing; you eventually, through the events of the games come to the conclusion that the Citadel, a giant space station which is the central hub of the entire galactic community, is also an ancient piece of Reaper technology used to control the technological growth of all space-faring races, which is also the final piece of the puzzle to activate and use said ancient weapon.
So at the end of the game Commander Shepard (the main character), who some how in the course of 3 god damn years and 3 games hasn't gotten promoted by the cosmic space army even though he/she has saved the galaxy like 4 god damn times, is given a few ultimatums: one is to control the Reapers at the cost of his/her own life by fusing his essence with theirs. Another is to destroy the Reapers as originally intended and as a consequence all other synthetic life including Commander Shepard as he is partly synthetic after the events of the second game even though the possibility exists that one day organic life may create synthetics that could one day surpass and destroy them...again. However a third option exists which is synthesis: the fusion of all organic and synthetic which would effectively put an end to the organic vs. synthetic conflict, again at the cost of Commander Shepard's life, cause why not.
Now the endings themselves aren't really that bad, the problem lies that literally no closure is provided by any of them as to what the fuck happens to every one after these events occur, don't know if everyone is dead, don't know if everyone is alive, don't know if everybodys' chillin in the Borg collective. It also doesn't help that all three ending cut scenes are the same no matter which option you pick in fact the only thing that really differs is the color of the ensuing end-game explosion; control = blue, destroy = red, synthesize = green.
Also some other stuff happens I guess, there are some robots with flashlight heads, one has sweet ass eyebrows, Martin Sheen is a villain and there is an alien who sings Gilbert and Sullivan.