ZX3 Story Outline

Here is the outline for what I think a ZX 3 should/could be
Set-up
The player chooses which A Mega Man they will play as
In this setting, it is revealed Thomas has gone rogue at some point between the games and has been attacking civilization with legions of mavericks. Legion is solely helmed by Mikhail now, who is working directly with a new organization made from the unification of the Guardians with the Hunter Guild and the Raiders. This organization is known as Peacekeeper and is lead by the ZX Mega Man, who has been unable to transform due to the loss of the Z Biometal and the ongoing repairs of the X Biometal due to an unknown incident that led to it being damaged. In order to allow the populace to escape the Maverick attacks, Legion is building a new city in the sky called Olympus, which is near completion. It is here our story begins.

Arc 1
The game starts with the A Mega Man being called to stop a mechaniloid near a bridge. After destroying it, the A Mega Man notices mysterious objects fly and scatter around the world. These objects have a Biometal signature.

Dubbed the Model C (for circle) by Mikhail, he tasks the Peace Keepers to find them. Not only that, there are 4 Pseudoroid readings, all in various energy hotspots. The A Mega Man hunts the Model Cs and the Pseudoroids down. These Pseudoroids are also powered by Model Cs.
During this, the A Mega Man finds either Prometheus or Pandora (depending on if they are Ashe or Grey), though the W Twins are now wearing a visor. They do not speak and upon being defeated, they flee. After dispatching the Pseudoroids, they are called to stop another Pseudoroid attacking the Peacekeeper base.
Unfortunately, they are overwhelmed and defeated, thanks to the Pseudoroid being more powerful than the others, and is accompanied by the 4 evil Mega Men. However, before the A Mega Man can be killed, they are saved by the X Mega Man at the nick of time, who wards off the foes.

Arc 2
As the A Megaman is recovering from their injuries, the X Megaman prepares to hunt down the evil Megamen, and are joined by Prairie, who navigates them on missions. They hunt down the evil Megamen and defeat them one by one. Upon each’s defeat in their Mega Man form, it is revealed they are also powered by Model Cs (multiple, in fact), which go berserk and transform them into monsters, similar to the Guardian’s Armed Phenomena. Regardless, the X Mega Man defeats them, afterwards the evil Mega Men explode and die after one last conversation with the X Mega Man, leaving behind their biometals.

They then hunt the Pseudoroid who attacked the base, which eventually reveals that it's powered by the Z Biometal. After a tough battle, the Pseudoroid reveals its true form, only to lose again. Before the Pseudoroid can kill the X Mega Man, it is paralyzed by a Cyber Elf, which allows the X Mega Man to kill it. The Cyber Elf reveals he is Giroutte, who was able to return to the mortal world due to gateways to and from cyberspace being opened by the Model Cs. Giro departs, and the X Megaman becomes the ZX Mega Man once more, as the A Mega Man recovers.

Arc 3
Thomas reveals that he has taken over Legion HQ, and has it protected by walls that cannot be destroyed until after his final 4 Pseudoroids are killed. These Pseudoroids are also attacking various parts of the world, and the two Megaman hunt and destroy them. Afterward, they travel to Legion HQ, only to be stopped by the W siblings, who are defeated and disappear. Throughout this series of events, they collect more Model Cs.

Basis for endings
They all have the same setup. The two Mega Men assault Legion HQ (alongside refights with the Pseudoroids) and make their way to Thomas, who transforms into a Model C Mega Man with the 8 Pseudoroid Model Cs he steals from the duo. He is unable to beat them though and is killed. The ending is based on how many Model Cs you collected. There is a max of 108 (with 8 being those from the Pseudoroids).

Bad Ending (No more?) (if you have 58 or less)
The Mega Men free Mikhail, who follows them outside the tower, where they plan on collecting more Model Cs, as a sinister vibe is given off

Good Ending and True Ending basis
After freeing Mikhail, Model C suddenly goes berserk, and attacks Mikhail. Mikhail captures it in retaliation and imprisons the Mega Men with energy cages. It is revealed that after the secret ending of ZXA, Thomas brainwashed Mikhail to make him think like Thomas, effectively allowing him to manipulate both sides of the conflict. He also reveals Model C's soul is that of the maker of the 6 Guardian Biometals, who Serpent captured for Albert after blowing up the artic Guardian Base. Her mind was trapped in Cyberspace until Thomas took it out and divided it into many pieces that were stuffed in the Model Cs.

(Now with Mikhail being referred to as Thomas) Thomas summons the W twins to kill the Mega Men, only for the W twins to be killed by the real deals. The W twins seen throughout the game were copies made by Thomas. The 2 W Mega Men fight Thomas, which frees the A and ZX Mega Man, who are tasked to flee, which they do. After fleeing, the A and ZX Mega Man witness Olympus moving towards the glaciers. It is also beginning to radiate lots of heat. It is becoming clear that Thomas wants to melt the glaciers and flood the Earth!

Luckily, it takes a lot of time to reach there, so the Peace Keepers plan to destroy Olympus’s forcefield to allow the Mega Men to enter the city and disable it before it reaches the glaciers. They manage to destroy the forcefield, but the Peace Keeper’s fleet goes down in the process. The Mega Men fight a horde of Mavericks onboard Olympus, now displaying Cyberspace architecture. They reach Thomas who confirms that his plan was to flood the current world and make a new one on Olympus, populated by "humans" that are biometal-powered robots with human limbs. The combination of the reploid immortality program and the Model Cs would make his world eternal. The Mega Men fight Thomas who becomes a C Mega Man and they succeed in killing him.

Good Ending (No more Mega Man) (If you have more than 58, but not all 108, Model Cs)
Model C then flees as the other Biometals destroy Olympus at the cost of themselves. Model C becomes a new threat to the world, turning robots into mavericks, which the former Mega Men are prepared to fight in an era of no Mega Men.

True Ending (No more Mavericks) (If you have all Model Cs)
Model C returns to her true self and deactivates Olympus's thermal engines, rendering it harmless. The Biometals then depart so their power cannot be misused anymore and so they can protect the Cyber World. Before Model C leaves, she activates the new race Thomas tried to control, who are soon welcomed by the Peacekeepers and dubbed the Cielians by Prairie, in honor of Ciel. The Mega Men then choose to adopt one young-looking Cielian, who they name Giro in honor of Giroutte.

A new era is born, one without biometals or mavericks, populated with humans with robot parts, human-like robots, and robots with human parts; who all live in a peace maintained by the Peacekeepers.

Miscellaneous Details
It would be revealed that Prairie did get caught in the raid that led to the 4 guardian biometals being taken by mavericks. After being healed in between the games, she eventually left on a self-imposed mission to find Ciel. She was the one responsible for reviving the dead W Twins with the Ciel System.

Several foreshadowings to Mega Man Legends era would be present, such as Olympus being a prototype of Elysium, the Cielians basically being prototype carbons (artificial life with organic elements). While not canon to the events ZX 3, secret disks that could be found in “new game plus” mode (after getting the true ending) would explain how the flood actually occurred, how humans populated the moon, and how the Cielians inspired the creation of Carbons.