The story... well, the story is better experienced than summarized, but it has to do with the nature of the universe and the meaning of life. There's kind of a substructure that deals with the whole "good vs. evil" dilemma, but not in the usual way. Religion is deconstructed, reality is warped, and it's difficult to tell the good guys from the bad guys. The Apocalypse also makes an appearance.
The Invisibles is also designed to change the reader, so be forewarned. If you stick with it, by the end you might find that it's less fiction than it is biography... Your biography.
Morrison (who has moved on to do mainstream comics like the X-Men and the Justice League) drew on an extremely diverse set of sources for his epic, including the Gnostic writings of early Christianity, the drug-fueled speculations of Terence McKenna, Mayan and Aztec religions, the Roswell crash, the Holy Grail, the Cathars, legends of the Knights Templar, the rituals of Freemasonry, Maya Deren's writings on Voudoun, the mad science of Wilhelm Reich and Jack Parsons, the cool '60s spy stylings of The Prisoner, the metaphysical posturings of Aleister Crowley... well, the list goes on.