Bored, I decided to write a story focusing on the events in-between Megaman Zero 4 and Megaman ZX. Take note, a few things you'll need to know of that happened but weren't shown in the games which were modified by me:

Harpuia, Leviathan and Fefnir are supposedly still alive.

Copy X seems to have just dissappeared off of the planet.

Phantom's mind is trapped within a computer somehwere.

Also, I haven't played MMZ3, so I'm relying a bit on the Megaman wiki because of this like that.

"Miss. Ciel!" A reploid shouted, running in the direction of a human girl, no older than seventeen years. "We have located an old factory, as well as several computer signatures within it." The human, Ciel, raised an eyebrow.

"Is it the factory that…?" She began, hopes obviously rising. The reploid nodded in response. "Yes, do you wish for us to land?"

Ciel nodded. "Yes, I expect a force of no more than six reploids armed, and to wait for me at the landing spot in thirty minutes." The reploid nodded and saluted, before running off.

Ciel looked outside of the flying craft she was in now, and smiled a warm smile. "Could it be?" She asked herself, breathing heavily. "Have we finally figured out a way to bring them all back…?"

A reploid dressed in red armour walked into a forest, absorbing the air around him. He walked up to a pair of metal doors before pulling out a small buster with an object of some sort lodged into the back of it. The buster began to glow before sending out a huge, fiery blast at the doors. Putting the weapon away, the reploid ran at the doors, before ramming them down.

The room was dimly lit around him. On one side of the room was a huge computer, on the other side was a huge incubation vault of some kind. Inside this vault was a small glowing elf of some sort.

The reploid smiled. "X… I knew you wouldn't die on me."

A blue reploid walked into a giant forest, a halberd strapped to her back. She scanned the area, before walking to a tree. "Harpuia," she said, her voice sounding jolly. "It's just the two of us, if we were humans we could enjoy ourselves fully and no one would notice." A green reploid, Harpuia, fell down from a branch, facing the blue reploid.

"Ha-ha, very funny Leviathan." He said to her. "What's the status on the location of Fefnir?" He asked her, his voice emotionless and stern. The blue reploid, Leviathan, puffed her cheeks.

"We could be doing so many naughty things, and you just sit her wanting to talk about Fefnir… I wouldn't be surprised if you were homosexual and just wanted to do the naughty things with our brother." She replied, her flirtatious mood ruined. "Anyway, I haven't found anything really closely linking him, but I have discovered what looks to be his helmet." Leviathan then produced a red and white helmet with yellow spikes on it which Harpuia took.

Studying the helmet, he nodded at Leviathan. "Yes, this is it." He said to her, looking up. "This is his trusty helmet, he'd never leave this just laying around. Maybe he's…" Harpuia broke down for a second then, his face showing a sad expression before he started making sobbing sounds. Leviathan came up to him and hugged him. "I'm sorry, Harpuia… I was sad when I saw it too, but we have to keep on living. That's what he'd want…" Harpuia slowly began to nod. "It's just… First Phantom, and now Fefnir. Who else must we lose?"

A dark figure loomed over a giant crater. Giving a hand signal, several reploids ran into the crater, scouting the area. Another of these reploids stood next to him. "No traces of life detected… Standing by…" The man nodded, before pulling out a laptop and running a program on it. A phrase slowly came into view on the laptop, "M.E.G.A System". The man smiled, before linking the laptop up to a strangely shaped rock.

"Sir!" the reploid beside him said. "We have just found Data 017!" The man nodded. "Bring it in, please." A few minutes later, a reploid ran in, holding out a blue gem of some sort. Nodding, the man placed the gem onto the strange rock. After half an hour, the laptop showed a "complete" screen.

The man picked up the rock, and shouted out, "Megamerge!" The rock glowed, and an electronic voice came from it, "Biolink Established. M.E.G.A System, Online." A ray of light struck down on the man, before disappearing as suddenly as it came, revealing a red Megaman in his place. "It is time…" He said, before walking off.