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The first stage, the base of the tower. At one point, it splits in two paths. The standard path has lava and Drop Lifts. The alternate path requires the Crash Bomber to destroy the blocks in the way, and contains a large pit and Foot Holders, and an Extra Life blocked by a rock that must be removed with Super Arm or Thunder Beam. Either way, Rush Jet and other transport items can make those passages easier.
The second stage. Near the beginning there is a room with a ? Can that requires the Crash Bomber to be accessed. It has alternate paths.
- Changkey Maker
- Kaminari Goro
- Sniper Armor
- Boss: Iron Ball
Wily Stage 3
The third stage. It has an alternate path that is blocked, requiring the Hard Knuckle to be accessed.
- Electric Gabyoall
- Giant Springer
- Hammer Joe
- Metall DX (propeller type)
- Needle Press
- Bolton and Nutton
- Pickelman Bull
- Returning Monking
- Boss: Buster Rod G
The final stage, a short area. Proto Man appears to open a path for Mega Man.
In the comic, the Wily Tower is a research institute called Chronos Institute that is researching time travel, as evidenced by the appearance of a disabled Time Man lying in the corner on the first page. Dr. Wily invaded the institute with the Genesis Unit and the Mega Man Killers to take over a time-travel device. Using the device, Wily remodelled the institute into a fortress. Shortly after, Mega Man appears to stop Dr. Wily, and he is hit by the device's energy, which sends him to different time periods.
- The paths shown in the game's map doesn't correspond to the stage's layout. For example, the map shows that the last stage's path leads to the top of the tower, but the stage is mostly a descending area. It also doesn't reveal alternate paths.