A biological warfare accident, retrovirus mutation, nanotechnology accident, bioengineering, or GMO accident could result in making human Y chromosomes inviable.
Or GMO effects might result in Y chromosome effects being moved to other genes, which might (?) result in female traits developing even in men.
Anything that results in men having female hormones in their system, and/or a lack of male hormones, will have some female rather than male traits occur in men, including breasts, no male-pattern baldness, and reduced facial/body hair, as well as altered behaviour (e.g. aggression and libido), and a wide range of other effects. You can get a lot of details on this by reading up on real-world transgendered people receiving hormones of the other gender.