I know it's been done to bits, but here's my take on a transitional game to go from Classic to X series. I will be honest, I'm not 100% versed on Mega Man canon, so I tried my best with the hope that I didn't screw much up.
Mega Man - Century's End
Aries Man
Weapon: Aries Hammer
Weakness: Strike Pincer
Libra Man
Weapon: Wind Scale
Weakness: Aries Hammer
Taurus Man
Weapon: Bull Rush
Weakness: Wind Scale
Cancer Man
Weapon: Strike Pincer
Weakness: Bull Rush
Intermission
Wily invades Light's lab, kidnapping Roll and stealing much of Light's data and robot plans. Much of the lab is destroyed, with Auto and Light left in a secret panic room.
Leo Man
Weapon: Flame Claw
Weakness: Aqua Cannon
Scorpius Man
Weapon: Venom Stinger
Weakness: Flame Claw
Capricorn Man
Weapon: Horn Spear
Weakness: Venom Stinger
Aquarius Man
Weapon: Aqua Cannon
Weakness: Horn Spear
Wily Fortress
Mega Man and Rush approach the Wily Fortress, and are met by Bass and Treble. The two transform into their Super Adapter and Treble Booster forms and fight, then Wily's voice is heard over a loud speaker. He states how fed up he is with Bass continuing to fail in his attempts to destroy Mega Man, and for Bass being a thorn in his side on several occasions. Wily charges a huge beam cannon and fires at the two. Rush and Treble disconnect from their partners, and together block a huge amount of force from the beam before being completely destroyed. Bass realizes Treble was the only thing he cared about, screams in rage, and teleports out. Mega Man is stunned, speechless, until something clicks. He shows anger for the first time and rushes toward the Fortress.
1st Boss: Ophiuchus, the snake bearing robot.
Bass appears and delivers the finishing blow to Ophiuchus. He explains he's going to take Wily down, and Mega Man should stay out of the way. He blasts the wall open and dashes in. Mega Man follows. There are two paths, a high one and a low one.
2nd Boss: Pisces, two aquatic shape-shifting robots. If you took the top path, the Pisces robot you face will be able to transform into Gemini Man , the bottom path's Pisces is able to transform into Centaur Man. Whichever you defeat, Bass is assumed to have defeated the other.
Wily appears through the ceiling, holding Roll hostage. Bass goes mad and starts to fire without hesitation. Mega Man grabs his buster arm, making him miss and hitting the support of Wily's platform. Bass tosses him aside, reminding him not to get in his way. Proto Man appears, grabbing Roll. They jump off of the platform as Bass jumps up toward Wily. The platform collapses around them, with Proto Man, Mega Man, and Roll narrowly escaping. The whole fortress begins to rumble, and as the three attempt to run out, red slime shoots out of the ground, surrounding Roll and Proto Man. They're dragged through a tunnel as the central part of Wily's Fortress is revealed to be a rocket, blasting off into space.
Wily Space Station
Mega Man returns to the lab. Dr. Light has tracked the rocket to a space station. He builds a teleporter extender to transport Mega Man onto the space station, but tells Mega Man it won't be able to get him back, that he'll have to find his own way. Mega Man steps in and is transported to Wily's Space Station.
1st Boss: Roll is standing in a room, back to Mega Man. When Mega Man begins to approach, she becomes surround in the red slime, assuming the form of the red Virgo Devil. Mega Man is forced to fighter her, and he does so until she is too weak to fight. Mega Man refuses to deliver the finishing blow when Proto Man appears, his yellow scarf missing. He teleports away with Roll.
2nd Boss: Proto Man stands in Mega Man's way, keeping him from going further. A screen in the background turns on but is just tv-snow, with Wily being heard (or text only). He states how it would delight him to see which of Dr. Light's fighting creations was the strongest. Mega Man fights him to a stand still, when the red slime returns and binds Mega Man. The screen turns back on, still snow. Wily explains how he reprogrammed Roll and Proto Man with ease when finally the screen clears up, revealing Wily now being fused with Bass. He explained how he felt that Bass's power was too great to waste by simply destroying him, and with the collapse of the platform handicapping Wily's body, he decided to use Bass's body to replace parts of his own. He then explained that as he had reprogrammed Roll and Proto Man, he would do the same to Mega Man.
In a lab, Mega Man is on a table, his mechanical parts open. Dr. Wily is talking to Roll and Proto Man, explaining that if he could not remove the binding laws of robotics from Mega Man as he had with Roll and Proto Man, he would simply install a chip to override them. Wily leaves a computer to finish the work. Cut to Wily on the control deck of the space station, Proto Man and Roll behind him. Wily gloats about finally winning when Mega Man walks in from a door in the background. Wily turns to revel in his accomplishment when Mega Man fires in his direction, Proto Man pushing Wily out of the way. Wily shows his surprise, asking Mega Man if he escaped before being reprogrammed, how he could have shot at him without hesitation, since he was still a living human. Mega Man explains that Wily was successful, revealing the override chip on the forehead piece of his helmet. But his original programming was still active, and now the two programs conflicted with each other. He explained how he now has the capacity to end it all. Wily commands Roll and Proto Man to destroy Mega Man as he escapes, the chair being a hidden elevator. It's revealed that the Space Station is losing control and is descending toward the Earth.
Fight: Roll and Proto Man together. Mega Man is a lot stronger now as he no longer holds back his full power. Both Roll and Proto Man are destroyed by the end of the fight.
Last Boss - Wily Bass: Mega Man tracks Wily down in the Space Station. Wily fully assumes the form of Bass, but the fins being red instead of yellow, and with silver hair coming out from under the helmet. Wily is completely destroyed. The Space Station crashes into the Earth. Mega Man as we know him is no more.
Cut to a dark lab. A capsule is revealed in the lab. From inside the capsule, a voice is heard. Cue Wily's lines from Zero's intro in X4. A pair of eyes open, the green irises glowing.
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