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A Japan-exclusive three-disc game, Super Adventure Rockman differentiates from the other games in the series by making it a first-person shooter and an FMV game. The two "modes" are boss battle and full motion video. The boss battles are in first-person and generally have old Robot Masters or enemies, although there are a few exceptions in which the player needs to fight new bosses exclusive to this game. Full motion video is much like Dragon's Lair in which the player must hit the correct button at the correct time to save themselves, although in this game missing the time does not lead to death always.
Usually after a boss battle is over, Mega Man will pick up a weapon, much like other games. In addition to that, some bosses will drop cards that show boss info. If Mega Man gets defeated, one of the few Robot Masters from the first Mega Man will save him and ask him to not fight any longer
A large building, named "Temple of the Moon", appeared in the Lanfront ruins in the Amazon, and the United Nations went to investigate. However, there was a large field of energy around the temple and made all their transportation explode. This intrigued Dr. Wily, so he went to see Dr. Light about the issue. After seeing that the field was getting bigger, Wily insists Dr. Light and Mega Man to not do any research, as Wily wants to go by himself so he could clear his name and make everyone think he is good.
Wily went to the temple to find the energy, and after searching around, Wily discovered a supercomputer called Ra Moon. Ra Moon had been on the Earth for tens of thousands of years, but was put in the ruins by humans not long afterwards. When Wily discovered it, the field gets so strong that it got to the Light Laboratory and made Roll pass out during that time. The reason only Roll passed out is because she was a female robot. Dr. Light then finds that the field was getting to be strong to the point that all things electronic would die. With that, Wily then addressed the world through televisions, saying that he harnessed power from Ra Moon and that all robots need to surrender to Ra Moon and Dr. Wily in two weeks time. Immediately Light made Mega Man, Rush, and Beat all completely immune to the field so they can get over there without any interruption by that field and end Dr. Wily's new found super computer Ra Moon before two weeks are up.
When Mega Man attempts to find his way through the Amazon jungle, he is constantly stopped by Wily robots that all were remade by Ra Moon for Wily. During this time, the player must make an option on whom they are to battle. After continuous battling, both Mega Man and Beat reach the temple, but are again met by some Robot Masters. When they found Dr. Wily after a long process of fighting his regenerated Robots again, he forced his robots to attack Mega Man, but all of them changed their mind about him and wanted to only assist Mega Man now. Through pure fear, Wily then supported Mega Man. Ra Moon proceeds to unleash his new robot, Ra Thor, which is a humanoid robot much like the Robot Masters themselves. Once the robot falls, Wily proceeds to leave Ra Moon, seeing as the computer is now evil and wants to rule the Earth like it had planned. However, after Wily states how they win, Ra Moon unveiles its next Robot Master, New Yellow Devil. As the name implies, it is heavily based off of the Yellow Devil. After that is gone, to destroy Ra Moon at last, Mega Man risks his own life by using the Double Mega Buster which could cause him to overheat and die. Fortunately, the Double Mega Buster was a success (although Mega Man was temporarily knocked out), Ra Moon and the temple were obliterated by the excess of strength from the Double Mega Buster, and the field was also wrecked, making all electricity work again.
Alternatively if Mega Man ever gives up, the game will cut to the lab and show Roll putting her hand down, which means she died. Mega Man and Dr. Light hug one another and Dr. Wily watches and laughs very loudly about their emotion