I made this story cause i hated the way that the Megaman Zero 4 video game ended. While the begining of the story does contain a brief flashback to four's ending check wikipedia if you didn't play the game yourself.
Well, here ya go.

1 year after the events of Megaman Zero 4, Resistance Base: Ciel called out to Zero over his helmet link. “Zero, come back now! There’s no way to stop Ragnarok anymore!” Zero reached up to turn off the link, but first he said, “No, there is a way. If I take out Weil’s core, the explosion will take Ragnarok with it. Ciel… believe in me!” Static filled the channel. Ciel screamed into the static, “Zerooo!!”
Ciel woke with a start. She had been sleeping at her lab desk again. She muttered, “So it was only a dream.” She walked over to the lab’s window to look at the night sky as she did the night Zero disappeared. “Oh, Zero. Why did you have to go and leave me?” A voice came from the speaker next to her monitor. “Dr. Ciel? Yes? There is a strange energy signature near the base. I’m sending you the specs. Could you please examine it?” She walked sullenly back to her monitor. She said, “ Yes, of course”, even more so. As the data scrolled down her screen, she perked up slightly. “I’ve never seen this before. Do you have more data from the scanner” There was a pause as the soldier looked up from his screen. “Hang on ma’am. Someone is trying to worm their way through the energy gate. I’m going to go out and see what the problem is.
After the guard went to the gate, Ciel faintly heard the conversation from the speaker because sound seemed to echo. “Who…not any resistance troops I recognize… with Dr. Ciel…no need to get violent.” Then the wall behind her exploded. The last thing she heard before she blacked out was a scream, which was her own, by the way.
The thing that woke Ciel up was a kick in the back. She was lying in a cold building in the middle of the forest. A cold, low voice asked, “Finally awake. Scared? Well don’t even think of moving. There’s a gun pointed at the back of your neck.” He wasn’t lying. She could feel the cold metal. “Once my partner gets back, we have a few questions to ask you.” A reploid in a ratty cloak walked into the hovel from outside. Ciel’s first captor sounded annoyed. “I’ve been waiting, and what’s with the cloak? It’s not like she can see our faces anyway.” A sharp thrumming noise from a sword began to resonate. There was a dull thud as the decapitated human hit the ground. A pair of hands began swiftly untying the ropes binding Ciel’s wrists. As he did so, she said, “thank you for saving me, but who?” She was cut off when the stranger said calmly, “Objectives: Protect Ciel, Eliminate all enemies in the vicinity. Commencing Mission.”

If you want me to keep writing my story, make sure you say so. No point in continuing to write if no one is interested.