I have a story in mind..
As for endings I haven't given it much thought. Nothing is set in stone as of yet, however this is what I was thinking as a possibility.
For the first release of the game I would like to try and keep it simple. For character specific endings have four different endings. Similar to what EOH does where each group has it's own ending.
#1 Ending for the Good guys.
#2 Ending for the Wily made Robot Masters.
#3 Ending for the Dr. Light made Robot Masters.
#4 Ending for the Dr. Cossack made Robots Masters.