Shadow Man is a stealthy and powerful ninja-themed Robot Master that first appeared in Mega Man 3. Possibly alien in origin, Shadow Man was originally an unknown, deactivated robot discovered by Dr. Wily, who remodeled and reprogrammed him. The metal body of Shadow Man does not match any material found on Earth. He is a master of ninjutsu, and can summon a giant frog robot to ride on or small frogs to check areas for him (a reference to Jiraiya, a rogue ninja hero from a Japanese folktale, who mastered frog magic). Shadow Man's main weapon is the Shadow Blade, a large shuriken coated with a deadly liquid.

Gemini Man  is a Robot Master from Mega Man 3, created by Dr. Light and Dr. Wily. He is capable of doubling himself, and uses that power to confuse or overwhelm his opponents. However, even without a clone to help him, he is a very tricky opponent to deal with, especially when he brings his Gemini Laser into play. He is a narcissist, and likes to admire himself in a mirror or with his double. Gemini Man also has a hatred and fear of snakes, mainly because his weakness is the Search Snake. Search Snakes can quickly eliminate Gemini Man before he can use his Gemini Laser.

Snake Man is a tenacious Robot Master with a snake motif that was created to investigate narrow areas. He is the first Robot Master with an animal themed design. Snake Man is prudent and prefers to chase and corner his opponents, and attacks with snake-like missiles called Search Snake that crawls on surfaces. In Super Adventure Rockman, Snake Man appears in the underground passage in Episode 2, and he can dig underground to stay out of Mega Man's range.

Spark Man is a Robot Master from Mega Man 3 created by Dr. Light and Dr. Wily. He was originally created to charge electricity before Dr. Wily modified him to be a combat robot. Spark Man is designed after a spark plug, and does not have hands. In place of them are two high-voltage electrodes, capable of producing powerful electric shocks and firing off balls of pure electric energy, also known as Spark Shocks, that can immobilize opponents in their tracks.

Magnet Man is a Robot Master created by Dr. Light and Dr. Wily. He was originally created to collect scrap metal using his powerful magnetic forces. Dr. Wily modified him into a combat robot in Mega Man 3. Magnet Man's main weapon is the Magnet Missile, a missile fired from a launcher on his right wrist that follows enemies. He is also capable of pulling his opponents closer to him with his magnetic powers, so he can attack them from close-range. Sometimes he sleeps by hanging on ceilings.

Hard Man is a Robot Master created by Dr. Light and Dr. Wily that first appeared in Mega Man 3. Originally built for land grading, he has a hard, durable exterior made of ceratanium, making him very heavy, weighing about three tons. He can fire his hands, known as Hard Knuckles, and has a cannon built inside of his body, giving him the boost needed to jump. Due to his excessive weight, he can stomp the ground and cause a tremor, much to Mega Man's dismay.

Doc Robot K-176 is a boss from Mega Man 3 who has a number of different attachments and devices on his body. After defeating the eight Robot Masters, Mega Man has to return to the stages of Needle Man, Gemini Man, Spark Man, and Shadow Man to fight against Doc Robot. He uses the powers of all the eight Robot Masters from Mega Man 2, utilizing their program data combined with his specialized devices.

Kamegoro Maker is the boss of the first Wily stage in Mega Man 3, an invincible machine that moves on a rail. It releases robotic turtles called Kamegoros into the water and controls them. Five Kamegoros must be destroyed to cause the Kamegoro Maker to self-destruct. As for the Kamegoros, if one is left alone long enough, it will actually shed its shell, turning itself into an explosive projectile and swim faster. The Kamegoros were originally created to verify the quality of water.

As Mega Man destroys a Kamegoro, the health meter of the Kamegoro Maker will deplete much quicker for each one destroyed. The Kamegoro Maker will lose two bars of health for the first Kamegoro destroyed; three bars for the second one; five for the third; eight for the fourth one, and the last Kamegoro will deplete the last ten bars of health for the Kamegoro Maker.

Yellow Devil MK-II attacks by splitting itself into parts and moving them fast to the other side of the room, hitting the opponent in the way of the parts and reassembling after all parts reach the other side. When it moves to the right by the first time when entering the room and moves to the left, it splits into 24 parts that move one at time from one side to the other. When moving to the right side for the second time onward, he combines into five parts that bounce to the other side. When assembled, his eye appears and shoots at Mega Man three times before moving to other side. Like the original Yellow Devil, he can only be damage on the eye. He is weak to the Hard Knuckle. Shadow Blade also does considerable damage to him, and as its speed is higher that the Hard Knuckle, it can be used to defeat Yellow Devil MK-II earlier.

Holograph Meha Mans, is a Copy Robot with a pair of holograms of himself. This Copy Robot only copies appearance, he does not copy weapons and moves, as he can shoot in any direction with the Mega Buster. Each copy walks back and forth on the platform it's on, occasionally shooting. After a while the holograms will switch positions. Only the true Copy Robot can be damaged -- shots pass through the other two. The Top Spin can destroy it in one hit, but the Search Snake is also effective.

The Copy Robot will always start on the uppermost platform. If the player is fast enough, they can reach and use the Top Spin on him before he changes places even once.

• There is a way to tell which Copy Robot is the true one. The fake ones will just appear from thin air while the real one has the teleport effect. It is similar to when Mega Man teleports in at the start of a level.
• The Copy Robot is one of the few bosses that does not have an invincibility frame after being damaged.

• 1st: Its weak point is the gun under it. The gun shoots energy balls that spin throughout the screen. The gun is weak to Hard Knuckle and Spark Shock.
• 2nd: Its weak point is the dome Dr. Wily is inside. Hit him when he goes down to smash, or use Rush Jet in order to reach high enough to hit him. One can also use Hard Knuckle (as well Search Snake), which is the second form's weakness. When destroyed, it is revealed that the Dr. Wily inside of it was a fake, and Mega Man will go to the last level to fight against the final boss, Gamma.

Gamma   is a giant peacemaker robot constructed by Dr. Light and Dr. Wily. During Gamma's construction, Dr. Wily feigned peacefulness, gaining Dr. Light's trust and assistance long enough to complete the big robot. Dr. Wily's true intentions were to use the enormous creation as a weapon, furthering his evil plans for world domination.

Gamma is the final boss in Mega Man 3. In its first form, it has a small blue head that shoots from its mouth. The simplest way to defeat this form is to stand directly underneath the head and use Shadow Blade. Alternately, the head is also weak to Hard Knuckle. After destroying the small head, Wily completes Gamma's head and controls him, attacking with shots and punches. Gamma's second form is very vulnerable to Top Spin, and can be defeated in seconds by using it rapidly against Wily. If desiring more of a challenge, use the Search Snake.