Dr. Wily was at one time Dr. Light's colleague in the Robert University of Technology, however he became a bitter rival during their professional lives. Wily and Light created many robots, being responsible for advancements in the field of robotics. Though Wily won many awards in his time, he was consistently upstaged by Dr. Light, and this wounded his pride. Tired of being one step behind Dr. Light, he moved to the Pacific Ocean and created a giant robot factory to set out to rule the world. Wily went missing for a long time.
Meanwhile, Dr. Light completed Proto Man, the first humanoid robot with feelings. However, Proto Man had a defect in his Solar Reactor, and he left Dr. Light's lab fearing to be changed, wandering around the world on his own. Dr. Wily came across Proto Man (who is presumed to have fallen unconscious or broken) and modified him, giving him a new nuclear core and additional equipment. Unfortunately for Proto Man, a defect still existed in his reactor. Dr. Wily continued with his plans to conquer the world, while Dr. Light continued creating robots to help humanity. After an unknown time, Wily enacted his evil scheme: exclaiming he would achieve this by stealing six (eight in Mega Man: Powered Up) of Dr. Light's industrial robots and reprogramming them.
During the events of Mega Man, Dr. Wily used Dr. Light's robots to take over the world. One of Dr. Light's robots which Wily saw no potential to be stolen and reprogrammed asked to be changed into a combat robot to stop Wily's evil scheme, and he was transformed into the super robot Mega Man. Mega Man stops Wily's robots and defeats him.
Note: In the North American instruction manual of the game, it is said that Dr. Wily was Dr. Light's assistant and the game takes place in the city Monsteropolis. This was something the localization team made up at the time as the Japanese version made no mention of any particular place.
Mega Man 2Edit
Dr. Wily returns in the second game trying to get revenge, this time creating eight of his own robots to defeat Mega Man, but his plans are foiled once again.
Mega Man 3Edit
Dr. Wily pretends to have changed his ways and helps Dr. Light build Gamma, a giant robot meant to bring world peace. But, he secretly reprograms the eight new Robot Masters (which he co-built with Dr. Light) to battle Mega Man, as well as creating eight Doc Robots. During the conflict, Dr. Wily steals Gamma and the Energy Elements and tries to defeat Mega Man. In the end, a block of debris from the Wily Castle falls onto Wily, supposedly killing him, but his flying saucer can be seen in the distance during the last scene.
Mega Man 4Edit
Dr. Wily managed to kidnap Kalinka, daughter of the scientist Mikhail Cossack. Dr. Cossack was blackmailed into using his elite robots to fight against Dr. Light and Mega Man. However in the middle of Mega Man's battle with Cossack, Mega Man's brother Proto Man teleports in with Cossacks daughter, Kalinka. The girl begs Mega Man to stop fighting her father and elaborating that Dr. Wily had kidnapped her and forced her father into building an army of robots. With Wily's plan undone by Proto Man's betrayal, he steps out from the shadows. Mega Man pursues his nemesis and fights through the newly built Wily Castle, but Wily manages to escape in the end.
Mega Man 5Edit
Dr. Wily tries to get revenge on both Proto Man and Dr. Light. He creates Dark Man, a robot with the ability to disguise himself like Proto Man to frame him. Dark Man kidnaps Dr. Light and lures Mega Man out to his doom. Unfortunately for Dr. Wily, the real Proto Man reveals that the other is a fake, and Mega Man defeats him. After defeating Wily, Mega Man frees Dr. Light and Wily's fortress begin to collapse. Mega Man holds the ceiling to avoid him and the two doctors being crushed, and Wily escapes. Proto Man later helps Mega Man and Light escape.
Mega Man 6Edit
Dr. Wily dons the persona of a billionaire named Mr. X (possibly having lived under the pseudonym for a long time). As Mr. X, he calls for a world tournament of the greatest fighting robots. He then reprograms the eight finalists and tries to use them to take over the world. When Mega Man defeats Mr. X, he reveals he was Dr. Wily and retreats to his Wily Castle. Mega Man goes after Wily and he is thwarted as usual, this time resulting in Mega Man sending him to jail.
Mega Man 7Edit
Dr. Wily knew he would eventually be imprisoned, so he had built four robots to search for him if they went without input for six months. He also built Bass and Treble sometime before his imprisonment. He was freed from prison by these robots and used Bass to get close to Mega Man. Wily was defeated once again in his new fortress, and Mega Man debated whether or not to finally kill Wily. After Wily reminds him that killing him would violate the First Law of Robotics, "No robot may ever harm a human.", Mega Man finds himself faced with a major internal dilemma. In the confusion, Bass helps Wily escape from Mega Man.
Mega Man 8Edit
Dr. Wily recovered 'Evil Energy' from a robot that fell from space. He used this energy to power his robots. Duo, another extraterrestrial robot hunting for the Evil Energy, helps Mega Man defeat Dr. Wily. Interestingly, when the Evil Energy starts infecting Mega Man, Dr. Wily actually seems shocked and horrified at what's happening, which implies that he didn't plan on the Evil Energy infecting Mega Man, but that he probably meant to surrender. Wily uses the opportunity to escape.
Mega Man & BassEdit
Wily was preparing his comeback, but was ousted from his new fortress by the robot King. Bass and Mega Man work together to defeat King, and it is later revealed that Wily created King, which was working according to his plans. Wily is later defeated again. In Bass' ending, Bass is angry that Wily deceived him, but Wily tells him that he now believes Bass is the strongest robot, and reveals plans for a King II, asking Bass to join King II to make them invincible and be able to defeat Mega Man. However, Proto Man appeared and destroyed the plans.
Mega Man 9Edit
Dr. Wily is shown in a flashback begging for mercy, apologizing for all the wrongdoings he has done in the past. In the present, he claims to have changed his ways for the good, yet mentions that Dr. Light has become a bad guy because Dr. Light's robots are causing havoc to the city, and shows a video proving that Dr. Light is the one responsible. Wily also states that he is willing to create robots to combat Light's evil robots, in exchange for donations. Dr. Light is sent to jail due to the accusations. However, after defeating the eight bosses, Mega Man finds proof that Dr. Wily persuaded the eight robots by telling them that they are on their expiration date and will be dumped, and reprogrammed them. Dr. Wily steals the proof and goes to his Wily Castle, and Mega Man goes after him.
After Dr. Wily's defeat, Mega Man recovers the proof and uses Rush to show nine of Wily's previous defeats. It is revealed that Wily used a fake Dr. Light robot to create the video and frame Dr. Light, and Wily tricks Mega Man into thinking the robot fake was the real Light. The fake Dr. Light electrifies Mega Man and Wily sets his base to self-destruct with Mega Man inside, but Proto Man appears and saves Mega Man. The ending states that Dr. Wily was nowhere to be found after the destruction of his base, and Dr. Light is freed. In the credits, Concrete Man is chasing Wily outside his base.
Mega Man 10Edit
When the Roboenza strikes most of the robots, including Roll, Dr. Wily goes to Dr. Light's lab and says he had discovered the cure, but the robots stole it and asks for help. After Mega Man got the cure, Dr. Wily got away with it and said he'd only give the cure for those who serve him. He also revealed that he had actually created Roboenza and infected the robots. He and his decoy were defeated in space, but he almost died because he was ill with human influenza, and had a fever. Mega Man got Wily to a hospital, where he disappeared after his recovery and left just enough medicine to cure all of the robots (In the Bass version of the game, Bass after defeating Wily left him to die from his infection from human influenza in order to "make him suffer," although it is implied that Mega Man managed to find Wily and take him to the hospital regardless).