Dr. Light has created a supercomputer designed to protect military bases from attack and shows a simulation of the computer's abilities. A general asks if Wily could destroy the computer itself. Dr. Light assures him that only a robot with great power could destroy the computer. Unknown to anyone Wily is listening to the conversation with the help of his "new pet".
Later on Megaman, Roll, Rush and Dr. Light are at a restaurant and Dr. Light is discussing the advancement of robot technology with Professor Henson. Suddenly, a huge spider robot bursts through the room and takes two waiter robots and starts draining their energy. Megaman tries to blast it but his hits don't affect the robot. The spider then leaves to drain the city's energy, Megaman and Rush follow. While the robot is draining the city's electric energy, Wily explains to Protoman that he plans to charge the robot until it is strong enough to destroy the supercomputer and ultimately control the world's military bases. Megaman tries to attack the robot but is sent flying by one of the robots legs.
After draining a monorail the spider searches for its newest target but is stopped by the police. Their attacks are futile and the spider drains the energy of the police cars. Dr. Light, Roll and Professor Henson see this and a run as the robot is chasing them! They are cornered at a dead end and the spider tries to capture them as Megaman comes and allows them and him to escape. While in the sewers they retreat to the university. There they discover that the spider's "web" is actually a wire that charges a battery inside the spider and Wily's plan. Then Megaman volunteers to copy the spider's components so that Dr. Light can make a device that can reverse the spider's powers.
Meanwhile Dr. Wily is draining the energy from the city's power plant after draining half the city. Megaman and Roll come to stop him. Wily sends Quickman and Gutsman to fight Megaman. He succeeds in defeating Quickman but is captured by Gutsman and thrown onto the spider's web!
Right before the spider drains Megaman, he jumps off the web, shoots a plasma blast at Gutsman which sends him into the web and he is drained of his energy. Megaman then copies the spider's web and leaves. Wily then sends out his tech-bots to find him. Megaman, Roll and Rush are now in the city and have to walk all the way to the University because Rush was damaged and Roll's Jet was destroyed. A tech-bot flying a helicopter traps them. Megaman is able to destroy the tech-bot and escape. Two more helicopters show up but Megaman destroys them as well. They are then confronted by spy bat-bots, Megaman destroys all but one. The spy bot reports to Protoman and Cutman about their location. They find them and start chasing them until they go into a museum. Megaman and the gang use the robot models to knock out Cutman, Gutsman and Quickman. Megaman then takes Quickman's power and uses it to trap Protoman. They then leave to meet with Dr. Light. But on the way they run into Brightman who blinds them while a tank is coming their way!
Before the tank got too close Megaman gave the spider data to Rush to give to Dr. Light "in case I don't make it". Rush leaves, Megaman tries to run but trips and falls. He then holds on the bottom of the tank and then blasts it and Brightman. Meanwhile Rush brings the data to Dr. Light. Dr. Wily meanwhile gets enough energy to destroy the supercomputer and rushes over to the military base. Megaman is given a device that can stop the robot. Wily then attacks the military base and is about to destroy the supercomputer until Megaman arrives. He topples the robots and destroys the robot spider.
Megaman uses the battery to bring power back to the city and congrats are given all around. The episode ends with Rush tripping on one of the spider's web and is given a jolt of energy. He flies all over the place before landing on the spider's web.