Well I think this will require some team writing and all. For one, Megaman Legends is completely not canon to the traditional Megaman line and so is Megaman EXE. Now for my plot... and my need for team of writers to help polish up my flaws and me theirs.
Zero will have his Megaman Legends version. I might make him part of the whole "Master System" and a close friend of Megaman Volnutt when he was still Megaman Trigger. Yup, he might have a history of being a former irregular unit until the Master managed to purify him. He helps Megaman Volnutt off from Elysium. In this version, Zero has pretty much the personality of his Megaman X counterpart. He will however have no Z-Buster but only his trusty Z-Saber which will have a powerful energy blade.
A Megaman Legends version of Sigma may suffice. In my own plot, this non-canon Sigma has been activated ever since Elysium was shut down. Long ago, Sigma was a true force to reckon once. Once an enforcer for the Master to hunt down abhorrent units, he has become one himself. Ruthless and sadistic, Sigma emerges to try and do what he always wanted to do- execute the carbon reinitialization program at the most brutal way possible. Sigma gives a command to Eden, which may soon affect the whole world. He will have a background story with Sera and Yuna, and how he manipulated Yuna all along to get ready for his return. I might call him as Dark Warlord Sigma (to differentiate him from the Sigma of the Megaman X series) who has also started allowing Reaverbots to attack the surface world as well. Sigma plans to recreate the world into a world ideally only for the strong, considering himself as the master of all the Universe giving him a true megalomaniac personality.
Meanwhile some buildup with the Bonnes can happen. Though the Bonnes are pirates, however they aren't as evil as Sigma who has resurfaced after some time hibernating, waiting. So pretty much, the Bonnes may actually become from enemies to allies in this fic. Data will soon reveal the whole process on how Sigma actually manipulated all the events that could lead to a Reaverbot apocalypse.
It's important for the first plot to rescue Megaman to which he is reunited with Roll and Barrell. Roll discovers about her missing father and for Yuna, she seeks to give Roll her mother back. The whole story may soon reveal some other non canon to the original Megaman. Maybe the whole story of carbons and humans can be elaborated or if there are any true living humans left on Earth. So far, it might actually require a backstory between Sigma and the Master. Sigma now wants to restore the Ancients but in his own image which this story may take some darker and edgier plots while maintaining some comedic approach.