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General
- A myriad of new enemies are present in the game. Several of them come from games released before Mega Man 4, and some even come from later games (up to Mega Man 8).
- The lifebars / HUD from the Game Boy Mega Man (Classic) games (also known as the Rockman World series) show up for the first half of Bright Man's stage. They also appear when fighting the Optical Capsule, the Petit Robot Masters and the Cockroach Omega
- Eddie will often show up alongside an arrow signaling either the next part of the stage or an oncoming threat, similar to his appearance in Navi Mode from the Rockman Complete Works and Mega Man Anniversary Collection versions of Mega Man 5 and Mega Man 6.
- Shadow Man is a Recurring Boss, appearing in Bright Man's stage, Toad Man's stage, Pharaoh Man's stage, and Cossack Stage 1. He also appears as a boss in Wily Stage 4 under certain conditions, as Super Shadow Man.
- When the secret bosses of the Robot Master stages are defeated, they're revealed to have been holograms, with the sprite used for the hologram being the same one used for the final boss of Mega Man 2. Dr. Wily also makes use of such holograms throughout Wily Stage 4.
- Balloon Adaptor functions like the Mega Man 3 variant of Rush Jet, allowing Mega Man to move in all directions while riding it.
Robot Master Stages
Bright Man
- One enemy in the stage uses the sprites of Chibee from Mega Man 3, but functions like the Hotarion from Spark Mandrill's stage in Mega Man X.
- Bright Man himself uses sound effects from Mega Man (the Thunder Beam sound effect) and Mega Man 3 (the sound that plays when the Elec'n enemy attacks)
Toad Man
- The first midboss of the stage is Gamarn and Gamadayu from Mega Man 6.
- Pole Eggs from Mega Man 3 appear, including giant versions that hatch into variants of Croakers from Mega Man 2.
- Shadow Man fights on the giant frog robot from from his Mega Man 2: The Power Fighters battle, using a sprite from the Rockman Battle & Fighters port.
Drill Man
- Gundrill from Mega Man V appears twice as a midboss in the stage.
- The Up'n'Down variants of the stage function like the Drill Moles from Mega Man & Bass.
- Quint appears as a midboss, and defeating him grants Mega Man temporary access to his Sakugarne.
- Making it to the end of the room right after Quint allows Mega Man to take an alternate path to get the Wire Adaptor, which is guarded by Crash Man from Mega Man 2.
- Drill Man's Desperation Attack causes part of the ceiling to collapse and potentially crush Mega Man, much like an attack used by Uranus in Mega Man V.
- The stage has a large number of references to Mega Man IV:
- The falling rock platforms from Pharaoh Man's Mega Man IV stage make an appearance early in this stage.
- The platform the Kabatoncue midboss stands on is made up of rows of rocks as opposed to a single segmented pillar, similar to its appearance in Mega Man IV.
- The room right after the Crash Man fight includes several of the destroyable missiles found in the Mega Man IV fortress stages.
- Finally, Drill Man's pattern consists of using floor-crawling projectiles while changing the height of the floor and ceiling (each seperated into four segments). This resembles the attack pattern of the second Hunter midboss from the final Wily Space Station stage (the main difference being that in Mega Man IV, the Hunter itself crawled along the floor).
Pharaoh Man
- If you use Toad Spell in the curse sections, the curse is immediately negated. In Mega Man IV, Rain Flush turned Pharaoh Man's quicksand into regular sand.
- The sinking platforms found in Uranus' stage in Mega Man V appear as obstacles early in the stage.
- The Kao na Gagnas from Mega Man 8 make an appearance, serving as stationary obstacles like in Mega Man & Bass.
- The aforementioned falling rocks from Mega Man IV also make an appearance in this stage.
- The room before the boss corridor features three statues, each modeled after a fire-themed Robot Master. They are, in order, Heat Man from Mega Man 2, Fire Man from the first Mega Man, and Flame Man from Mega Man 6.
- The T. Khamen midboss from Mega Man V appears at the very end of the stage, though it doesn't attack and goes down in just a few hits.
Ring Man
- The start and end of the stage feature non-lethal variants of the lasers found in Quick Man's stage from Mega Man 2.
- Ring Man's weapon, the Homing Control Ring Boomerang, can pick up items, similar to a function given to the original Ring Boomerang in Mega Man IV.
Dust Man
- Several pieces of scrap fall from the ceiling in the first room of the stage. Among the scrap is the falling blocks from Mercury's stage in Mega Man V, and an early design for the Giree enemy from Mega Man 5, found in the ROM of the latter.
- Dust Man's vacuum attack (sucking Mega Man towards him before then blowing him away while firing off projectiles) bears a loose resemblance to the main attack of Hyper Storm H from the Mega Man: The Wily Wars sub-game Wily Tower, with the main difference being that Dust Man also sucks in junk projectiles from off-screen.
Dive Man
- The first midboss of the stage is Hogale from Mega Man 8.
- The second midboss is Enker, and much like Quint, he gives a temporary version of his Mirror Buster weapon upon defeat.
- Also like Quint, holding onto Enker's weapon for two rooms after picking it up (and hitting a Jet Bomb in that room with it) opens an alternate path with Balloon Adaptor at the end of it, guarded by Wave Man from Mega Man 5. The obstacles preceding and following the fight are both from Wave Man's stage.
- Wave Man's battle also includes a subtle reference to another Mega Man game; when he Turns Red, he will start tossing water balls in the air in the middle of his jumps. This attack is lifted from a boss in Mega Man 3: The Robots are Revolting (released the same year as Mega Man 5) who is also named Wave Man.
- Dive Man's battle takes cues from the Wily Tower boss Mega Water S. The layout of the boss room is similar (a half-submerged arena with a hazardous pit in the middle, with a thin platform of the same length placed directly above the water), and Dive Man's Water Cutter can push Mega Man around, much like how Mega Water S tries to push Mega Man off the top platform of his arena with high-pressure water.
Skull Man
- Throughout the stage, a myriad of platforms from the six NES games (as well as the Move Hover from Mega Man IV) make an appearance. The Mega Man 6 platforms that appear are the flipping platforms from Wind Man's stage and the flying platforms from Tomahawk Man's stage. With the other five games, it's actually easier to list the platforms that don't appear.note
- The stage also includes two references to Slash Man's stage from Mega Man 7:
- Finding a secret pathway at the start of the stage leads to Beat, who's been locked in a cage that must be broken with a charged Mega Buster shot. This is a nod to where Beat is found in Slash Man's stage.
- The midboss of the stage is King Gojulus, the midboss of Slash Man's stage.
- The background tiles in the final stretch of the stage come from the Mega Man III version of Skull Man's stage.
- On Hard Mode, Skull Man will toss his Hell Wheel away when he crashes into a wall, causing it to roll to the ceiling and split into four small projectiles that fall off the screen. This is a nod to how Turbo Man uses his Scorch Wheel in Mega Man 7.
Fortress Stages
Cossack 1
- The latter half of Cossack 1 is an homage to the SHMUP-like Tengu Man's stage and Wily Stage 2 from Mega Man 8. It even has Mega Man riding Rush.
Cossack 2
- Square Machine's fight now combines its splitting capabilities with attacks directly referencing the X-Hunter Base battle against Serges from Mega Man X2, with the machine using various turret enemies throughout the fight, and Mega Man being given three small moving platforms to keep him from falling into a spike pit.
- Square Machine will eventually weaponize the infamous lasers from Quick Man's stage in Mega Man 2, with the turrets they're shot out of even being recolored background tiles from Quick Man's stage.
Cossack 3
- A split path is present partway through the stage. The upper path features the cracked water pipes from Neptune's stage in Mega Man V, while the lower path features a rising and lowering liquid that Mega Man floats to the top of, taken from Burst Man's stage in Mega Man 7.
- The Double Bubble Core turns out to be generated by copies of CWU-01P from the first Mega Man game.
- As a followup to the Square Machine battle, the battle against the Aqua Devil (which is a recolor of the Yellow Devil MK-II from Mega Man 3) references the battle against Agile in the third X-Hunter stage from Mega Man X2, though its attacks consist of much more than the falling rows of blocks that Agile uses.
Cossack 4
- The stage begins with a battle against the Nightmare Suzy, a pair of Giant Suzies (much like the one seen in Mega Man III) that behave like the Nightmare Mother from Mega Man X6.
- The four generators that must be destroyed to progress are actually repurposed tiles from the fourth Mr. X stage in Mega Man 6.
- The stage takes the Enker and Quint midbosses to their natural conclusion, with the other three midbosses encountered in the stage being the remaining Mega Man Killers (Punk from Mega Man III and Ballade from IV) plus Terra from Mega Man V. Yet again, Mega Man has the option of using their weapons when he defeats them (though this time he keeps them until he either picks up a weapon from one of the other two midbosses or completes the stage).
Wily 1
- The stage serves as a counterpart to the original Mega Man 4 Wily 1, with the idea of a stage consisting almost entirely of variants of a recurring enemy (ending with a battle against a King Mook of the enemy in question) being done with Sniper Joes in place of Metalls.
- The final stretch of the stage recreates the idea of Ride Armors from the Mega Man X games with various vehicles ridden by Sniper Joes throughout the series (namely those of the Sniper Armor from 2, the Apache Joe and Rider Joe from 5, the Cannon Joe from 6, and the Gunner Joe from IV).
- The boss, Joe Ni-Nin Va All, uses the sprites of the Sniper Joe 01 from Mega Man 7, and uses an upgraded version of the pattern used by Proto Man in his secret boss fight from the same game.
Wily 2
- The destructible orbs that block Mega Man's path throughout the second half of the stage are based on background objects from Bomb Man's stage in the original Mega Man.
- The device used to make Snatchman is the same one used to create the Copy Robot in the first Mega Man.
- The background in the final phase of the fight is a mix background tiles from the original Copy Robot battle and background tiles from the fifth Wily Stage of Mega Man 2.
Wily 3
- The special items found throughout the stage each have the face of a Robot Master on them (namely Ice Man from the first game, Flash Man from 2, and Magnet Man from 3)
- The tokens dropped by the Robot Masters in are taken from the first Mega Man. They are replaced by Yashichis whenever their rooms are revisited.
- The second phase of the Wily Machine 4 battle uses attacks from the Jet King Robo fight in Mega Man & Bass, with Rush serving the role of the platform Mega Man rides on to reach the machine's weak spot.
- Right after the Wily Machine 4 is defeated, Wily uses a trap to capture Rush before escaping. The trap uses the sprites of an emergency exit Dr. Wily used in Mega Man III.
Wily 4
- Each Chimerabot is a fusion of two Robot Masters from one of the first three Mega Man games:
- Chimerabot 1 combines the color scheme, movement pattern and spread shot powers of Elec Man with the appearance and boomerang projectiles of Cut Man.
- Chimerabot 2 combines the color scheme and movement of Quick Man with the appearance and projectiles of Wood Man.
- Chimerabot 3 combines the color scheme, bouncing projectiles, and cloning powers of Gemini Man with the attack pattern of Needle Man.
- The fusion of each Robot Master is visualized by one of them (doing a pose) falling onto the other, much like how Doc Robot indicates what Robot Master pattern it's copying in Mega Man 3. The scene is even accompanied by the intro of the Mega Man 3 boss theme playing before transitioning into the boss theme from the game the Chimerabot is based on (or simply continuing the Mega Man 3 boss theme in the case of Chimerabot 3).
- On Hard Mode, Chimerabot 1 will throw a cutter that rolls along the ground, climbs up the wall, then drops down before disappearing, not unlike Nitro Man's Wheel Cutters in Mega Man 10.
- Super Shadow Man uses several attacks that Hidden Phantom from the Mega Man Zero series uses, most notably riding on a ninja star while throwing clusters of kunais.
- The visceral second half of the stage uses several recolored tiles from Gemini Man's stage in Mega Man 3.
- All three of the enemies in the second half of the stage are based on Mega Man V:
- The Organic Slimes use sprites of Mercury in his blob form.
- The Organic Shaboans are red-colored versions of the Shaboan enemy from Venus' stage.
- The Organic Ball uses the sprites of the asteroids from the Rush Space sequence leading up to the Wily Star.
- Acid drops lifted straight from Wily Stage 6 of Mega Man 2 make an appearance.
