Y: The Last Man, Volume 9: Motherland
This is the one where we get all the answers. Vol. 10 is reserved for thematic and emotional cleanup, and Vol. 9 tells us the rest. Turns out Y is not the last man, he's one of two, and the other is Allison's father, Dr. Matsumori. He claims that it was his act of cloning Allison -- not himself -- that brought on the plague . . . and he's determined to finish the job. Both Matsumori and Toyota are taken care of in the end, but not before 355 is gravely injured. Allison's mother patches her up, but she won't be able to have any kids. This doesn't seem to be an issue until Allison points out that she's in love with Yorick, and has been for quite some time. But 355 keeps it to herself, and she and Yorick head to Paris to look for Beth, not knowing that Other Beth, Beth, Jr. (Yorick's daughter), and Hero are also headed there. Allison and Rose stay behind, as it's now Allison's duty to mankind to repopulate the Earth with Yorick clones until she can perfect the cure to the plague and bring back other men from the dead, clone-style.
I know a lot of people see these answers as a cop-out, but for me reading this series was never about finding an answer to what killed all the men. We also get to catch up with some old faces in the two one-shots that close out the volume. The Obituarist brings us back to that supermodel that Yorick met all the way back in Unmanned, and Tragicomic catches us up on the Fish & Bicycle acting troupe who were putting on theater productions The Last Man, but now are focused on film. When that flops, they turn to comic books, and the series comes full circle as they endeavor to "create something new, something that challenges our audience at the same time it's helping them escape." They create The Last Woman.