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In Neo World Three's base, Tesla Magnus is reading a newspaper article mentioning Viddy Narcy and Takeo Inukai being taken into custody. Fed up with the results, she demands that they use the last ace up their sleeve. Noboru Sunayama and Rei Saiko, the two remaining lackeys, leave to form the last piece of the puzzle for their plan. Tesla didn't even notice she was being watched by Dark MegaMan.EXE and his remaining Darkloid lackeys.
The crew responsible for manning the elevators is working on cleaning the space debris for the official public debut. They notice an unspecified shuttle is trying to land in the colony, but the craft has no clearance to dock in. It manages to enter. Neo World Three has made their way to the space elevator. Then, MagnetMan.EXE jacks in along with Asteroids FlashMan.EXE and DesertMan.EXE. Flash and Desert take out the security Navis allowing Magnet to manipulate the colony's core system. All of the power goes out. Coincidentally, Lan was in the restroom. Just when he finishes, he fell back in surprise of the power outage. Then, he finds that the electric-powered door is jammed. He can't get out! Not to mention his PET slipped out through the door when he fell.
Manuela and the NetPolice arrive to the elevator entrance. Just when things couldn't get any worse, the satellites meant for recycling ejected from the shuttles that were collecting them. Then, Tesla comes on the air all over the world from the space colony. Lan watches the broadcast from the restroom. She announces that she and her team are now programming the old satellites to head for a collision course to Earth's major cities. The colony staff is seeing a diagram of where the satellites tend to land. Targeted locations include cities within regions of Madagascar, South Africa, Saudi Arabia, somewhere in Eastern Europe, China, and quite possibly southwestern Russia. All are set to land and detonate in 30 minutes.
The NetPolice arrived to the scene with Neo World Three expecting them. Tesla reveals to Manuela that she let her and her squadron enter the colony so they can witness everything up close and personal. Noburo and Rei summon FlashMan and DesertMan with Dimensional Chips to attack the officers. Meanwhile, Lan tries to break out but is unsuccessful. Maylu comes to check up on him. He tells her to get him out, but Maylu is too cowardly (as well as too full of her young feminine pride) that she doesn't want to.
Only 20 minutes remain until doomsday. The satellites have already entered the atmosphere. The crew tries to find a self-destruct sequence for the satellites to detonate them before they enter the cities. Lan manages to persuade Maylu to help him. She rushes to go find something to break him out. She locates a long wrench and uses it athlete style to break open the door. She manages to break it up to the point where she needs a breather when she finished. Lan was stunned by her strength. Then, the two dynamic duos make their way to one of the thirty elevators to get to Neo World Three, but the power outage affected the elevators as well.
10 minutes remain. Lan decides to get to Neo World Three with a Dimensional Area. Lan is about to morph alone, but Maylu decides to go with him. Rush hears her call. And after some soft incentive, he transforms into a Synchro Chip. The two friends morph into Cross Fusion MegaMan and Cross Fusion Roll.
5 minutes remain They teleport down as orbs of light - blue and pink - to the enemy's location, bashing through the ceiling and wearing down DesertMan and FlashMan. They land ready to fight. Manella directs Lan to the control room. The Asteroid Navis are ordered to intervene. Lan goes in to attack FlashMan with Step Swords and a Search Gun, but that wasn't enough to defeat him. FlashMan gets the upper hand despite his bruises. Maylu is about to help him, but DesertMan uses the pink hybrid's distraction to his advantage and attacks her.
3 minutes remain. Maylu manages to get up stating her reasons to fight. She remembers Lan asking her to do something really important for him. She recalled being like a shadow of Lan, always standing one step behind him in battle. So she made up her mind: now she has attained Cross Fusion from Lan, she'll repay him for all he's done for her by helping him. With her newfound determination, she charges for Desert and summons a Rush Hole to kill him.
2 minutes remain. The blue hybrid gets up and clashes Flame and Bamboo swords with FlashMan's Shining Bulb Crusher. Everyone awaist the outcome... and FlashMan dies as well. Lan warps to the control room to demorph. He jacks MegaMan in to the computer to stop MagnetMan. The cops arrest Neo World Three; Manella stops Tesla just before she's about to use Cross Fusion. MagnetMan logs out as MegaMan stops him in time.
1 minute remains. The staff regains control over the satellites and they blow them up saving everyone. The dimensional area deactivates. Cross Fusion Roll powers down back to Maylu. Manella congratulates them on their teamwork saying the mission was a success. No one was hurt.
Dark MegaMan sends a D.A. generator to get Tesla! She reappears back in her lair. As for all of her four men who are now in jail, their memories are wiped clean through D.A. generators. Manella receives word of it which also surprises Lan.
In Lan's PET, a message comes through. It's Dark MegaMan in Neo World Three's base. He has Tesla as his hostage. He says he's also responsible for erasing the memories of her former lackeys since he didn't want any interference. He states that he wants to create and unleash his own fear and confusion to the world. He signs off leaving Lan to wonder what to do.
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