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In celebration of Mega Man 3's Virtual Console arrival, I am pleased to present my Tactics to the game's Robot Masters, the Dr. Robot bosses, and Dr. Wily's boss battles, as well as provide some passwords and secrets!  I hope this helps you get through one of my favorite games of all time!

The Robot Masters
1. Top Man
Top Man is my recommended first Robot Master for one key reason - his pattern is easy to pick apart after a few moments.  His first attack, which he sends 3 tops in the air, which he will send them to convene on your present location, can be dodged by a quick slide.  His second attack, when he spins on his skates for a few moments and then rushes across the screen, is also a simple matter of leaping over him as he dashes forward.  A quick note - Top Man's first self-spin is much faster than his subsequent ones.  He will then repeat this pattern.  Top Man is open to attack any time where he is not spinning.  So barrage him with Mega Buster shots during the 3 top phase, be ready to leap over him as he spins at you, and repeat until he's destroyed.  His usual weakness is the Hard Knuckle, which will crush him in 4 shots.
Reward - Top Spin

2. Shadow Man
Shadow Man normally is one of the game's most daunting Masters - his insane speed and random movements can make him very unpredictable and dangerous.  Thankfully, the Top Spin will subdue him in 4 spins.  However, there are two downsides: the first is that you will take damage per Top Spin, and there is a grim possibility that you will accidentally burn your entire Top Spin meter on any attack upon Shadow Man, forcing you to switch back to the Mega Buster and hoping that his spastic leaps will strike your weak bursts.  Outside of leaping around a lot, Shadow Man will slide across the floor REALLY fast or sling two speedy Shadow Blades at once (one straight forward, the other at an upward-diagonal slant).
Reward - Shadow Blade and Rush Marine

3. Spark Man
Before I begin, you could go one of two ways here.  I usually tackle Spark Man, since his stage is among the trickiest and getting it over with is rewarding, but you could also tackle Magnet Man at this point as well.  Magnet Man has the unusual property of being weak to two different weapons - the Spark Shock and the Shadow Blade.  But, for the sake of following my usual pattern, we'll discuss Spark Man.
Spark Man's room isn't flat like most of the other Masters - it features a pyramid like formation.  He'll leap around from platform to platform, and usually stop at some point (usually he'll be on the far side of the stage or on the tall centerpiece, but he can attack from the other platforms as well) to unleash two spark attacks.  His first is a cluster of small sparks that fly out in 8 directions.  His second is to charge up a huge spark and then throw it at your present position.  Considering the various heights this room contains, the Shadow Blade is a godsend.  Its ability to be thrown diagonally or straight up will be very useful for many parts of the game, and this fight is no exception.  It'll take 7 blades to defeat Spark Man.  Take advantage of his attack pauses to drill him with blades.
Reward - Spark Shock

4. Magnet Man
Magnet Man's dual weakness, as mentioned above, makes this somewhat tricky fight a cakewalk at this point.  Either weapon will knock out 1/4 of his life meter.  I recommend the Shadow Blade mainly for its ability to be thrown in more directions than the Spark Shock, but in the later Wily Boss Battle Rematch, the Spark Shock will probably make more sense for ammo conservation.
As for Magnet Man, he has two attacks.  He'll either create a magnetic barrier, which will pull you closer to him.  This also renders him invulnerable, so don't waste ammo while he's performing it.  His second attack is a barrage of Magnet Missiles thrown in the air.  He'll fire three of them, which will home in to your present position.  In between attacks, he'll jump once to cover about a 1/3 of the screen, then will leap the rest of the way to the room's wall.  He's most open when he's firing off missiles, so use the Shadow Blade's upward throws to subdue him quickly.  In the Wily rematch, use the Spark Shock as he bounds across the room or falls after unleashing his missiles.
Reward - Magnet Missile

5. Hard Man
Hard Man, despite his slow speed, can be a major headache to battle.  Thankfully, Magnet Missiles stick to him like glue, and 7 will be enough to conquer him.  The Missile's homing ability will prove to be quite handy here.  Hard Man's two methods of attack are the firing of two Hard Knuckles, which, in his case, have the ability to turn around and come back at you, or he will leap into the air and smash his mass into the ground, which will freeze the action temporarily.  He also usually follows his head stomp with Hard Knuckles, so keep that in mind.  Sliding is a good tactic to avoid the Hard Knuckle barrages.  Pressure him at any opportunity with Missile launches, and the match should be yours.
Reward - Hard Knuckle

6. Gemini Man
Here's where things get a bit screwy.  Capcom set up the Robot Master weaknesses in two sets, with the first five bosses I've discussed thus far being weak to each other, and then Gemini Man, Needle Man and Snake Man being weak to each other's weaponry.  It does make choosing the next stage to battle a little more complicated.  I find Needle Man to be the toughest standard Robot Master in the game, and Snake Man's stage geography making his battle tougher than it would be without the elevation switches, so I go with Gemini Man first in this set.
Without the Search Snake, Gemini Man will take longer than usual to go down.  He's quite difficult, as well.  However, Gemini Man has the unique attribute of firing small bursts upon you when you tap the fire button.  Keep that in mind as you take down his clone with Shadow Blades (again proving their worth) or with the Mega Buster.  If you do not attack, the two clones will simply leap across the stage and then dash back to the right wall very rapidly.  After his clone goes down, he'll jump when you press fire, so use that knowledge to your advantage.  He'll fire off his Gemini Laser randomly at this point, which will bounce off the stage's walls for a while before breaking apart.  It'll be a tough fight, but patience will be rewarded.
Reward - Gemini Laser

7. Needle Man
Needle Man is a spaz.  Even more so than Shadow Man is.  Despite the bulky armor, he is very mobile and very dangerous.  Thankfully, the Gemini Laser will cut him down in 4 hits.  Disabling him is easier said than done, though, thanks to his random leaps and his speed.  Try to aim the laser as he's grounded, leaping up slightly to fire it.  It'll double your chances of a clean strike, since he's in the air more than he's on the ground.  If you miss, try to avoid his two attacks, which are firing needles from the air and launching his pointy head plate at you from the floor (which has a long reach!) and hope that the beam's reflections will work out in your favor.  You can't fire more than one laser at a time, so the tension will raise thanks to the slow pace of the beam's bounces.
Reward - Needle Cannon and Rush Jet

8. Snake Man
The Needle Cannon helps make Snake Man a pretty easy fight.  Snake Man slithers around the room, and will occasionally leap up and fire off Search Snakes, which crawl along the floor and disappear when they reach the ceiling.  He isn't difficult on his own, thanks to his slow speed and his attack being so straightforward, but the stage's layout will be the tricky part.  Thanks to the various elevations, Snake Man is very hard to get around as he paces about his lair, and the Search Snakes move much faster than he does, and he's coming at you as you're trying to weave around them.  Rail him when he's not flashing, and the fight will be over quickly.  It takes 7 hits from the needles to win this fight, so keep the pressure on him.
Reward - Search Snake

Dr. Robot
Dr. Robot...is a Gutsman wannabe, merging with the powers of MM2's Robot Masters.  *shrugs*  These stages are among the hardest in the game, mainly because you'll have to defeat two Dr. Robots in one stage to pass!

Spark Man Redux - Metal Man, Quick Man
Metal Man can be tough, but quickly belt him with Magnet Missiles while avoiding the constant Metal Blade carnage he slings at you by timing slides or jumps to his attacks.  Other than jumping, he remains stationary, so he's pretty easy compared to some of the other MM2 bosses.  Spark Shocks also work well, but the Magnet Missiles can home in on Metal Man, so I prefer to use those.
Quick Man's speed is insane, and he loves to leap over your head and pester you with Quick Boomerangs.  4 Gemini Lasers will take him down, but it'll be a tough fight.

Needle Man Redux - Air Man, Clash Man
I find Air Man to be one of the toughest boss fights in the game.  His Air Shooter peppers the stage with mini tornadoes, and when they blow off the stage, it'll drag Mega Man with it.  On top of that, your attacks will reflect off of the tornadoes, making this a difficult battle.  Magnet Missiles are quite effective, but the Spark Shock will also work as well.
Clash Man will not fire off a Clash Bomb until you attack him, so be cautious when you use your Hard Knuckles to defeat him.  He'll leap and fire off a bomb when you tap the fire button, so keep that in mind.  4 Knuckles will be enough to defeat him.

Shadow Man Redux - Wood Man, Heat Man
Wood Man is a tricky boss to defeat.  His Leaf Shield will repel any attack, and the time he's open to attack is thin and filled with other obstacles to avoid.  Use the Needle Cannon to wear him out.
Heat Man can be very hard until you grasp his pattern.  He'll launch fire walls until he's struck, then he will ignite and fly across the room to where you were standing (and he's invincible during this phase).  To add to the aggravation, his fire walls can reflect bullets.  The Hard Knuckle and Shadow Blade work well against him.

Gemini Man Redux - Flash Man, Bubble Man
Flash Man's ability to stop time will make this a harder fight than you'd think, and the pyramid structure of his boss lair doesn't help.  Use the Needle Cannon to deliver the maximum amount of damage to him.
Bubble Man's lair is submerged, and the ceiling is loaded with spikes.  Watch your jumps as you bob around his Bubble Leads and fire off Spark Shocks or Shadow Blades to defeat him.

Break Man
Break Man is an enigma in the classic MM plotline...he only appears in MM3, and despite looking exactly like Protoman with a mouth plate, Protoman never again uses that plate for the rest of the MM series.  I'd like to think of him as a separate character, despite arguments that it was merely a disguise for Protoman...but I digress.
Break Man can only take damage from the Mega Buster, so save your other weapon ammo.  Do your best to avoid his blasts and bumping into him until he finally warps out from you attacks.

Dr. Wily's Castle
Kamegoro
This fight is quite simple - equip the Top Spin and hit each turtle as it appears.  You ought to be able to get through this battle without taking any damage, if you time it right.  If the Top Spin drains on you, use the Shadow Blade in its place.

Yellow Devil
This gigantic pain returns from the original Mega Man, and he's tough.  Hard Knuckles are very effective against him, but his only weak point is his eye, and it's rarely there.  The battle will begin with small blocks flying in from the right of the stage that you will have to dodge.  Slide or jump through the problematic ones, and be ready to launch Hard Knuckles at him when he finally unites.  I find that leaping in the middle of the room and aiming the Knuckles upward to be the best way to battle him safely.  When he solidifies, he'll fire small blasts at you from his eye, then will proceed to break down into 5 bouncing blocks and will go over to the right wall.  Then he'll fire some more blasts, and the cycle repeats, with him breaking apart and heading left again in small parts.  It takes about 7 Hard Knuckles to conquer him.  Make sure you save some of them for the next area though, as there will be some barriers to bust through!

Mega Man Hologram
Wily loves duplicating Mega Man.  Three tiers of platforms, each with a MM clone, is the lair's setup, and you can only damage one of the three doppelgangers.  While the Top Spin is most effective, I prefer to use the Shadow Blade here for two reasons - one is that the Top Spin will make the final boss fight (and the upcoming Shadow Man rematch) much easier, and that the Shadow Blade can attack above Mega Man, while you would have to figure out the right clone to use the Top Spin on before he teleports to a new position, which is frustrating.  Once you find the right clone, drill him with blades until he teleports, then find him again and continue attacking.

The Dr. Wily Robot Master Rematch Circus!
Here, 8 teleporters await to take you to the recently rebuilt MM3 masters you've battled earlier!  Capcom seems to get extreme pleasure in rehashing boss fights.  Anyway...here's a summary of what each Robot Master is weak to, and how many of them it'll take to beat them:
Magnet Man - Shadow Blade or Spark Shock (4)
Hard Man - Magnet Missile (7)
Spark Man - Shadow Blade (7)
Snake Man - Needle Cannon (7)
Top Man - Hard Knuckle (4)
Shadow Man - Top Spin (4)
Needle Man - Gemini Laser (4)
Gemini Man - Search Snake (7)

Dr. Wily Fake
Charge up the Search Snake and Rush Jet at the beginning of the stage.  After the left leg creeps in, sneak in under it and fire Search Snakes at the turret when it appears.  Spark Shocks or Hard Knuckles also work well here.  When it explodes, get back out from under the robot and consider using the Rush Jet to fire Mega Buster bursts at Wily.  You won't be needing the Jet after this point, so don't be afraid if it gets low.  If you run out, you can always sling Shadow Blades at Wily.  One more battle to go...

Gamma
Make sure the Hard Knuckle and Top Spin are full before battling Gamma.  Climb up to the top right platform and get as far right as you can get, then stand and fire Hard Knuckles at the blue part of Gamma's head by steering them upwards.  After a few blows, it'll explode, and Wily will fall in with the true headpiece of Gamma.  
Equip the Top Spin and strike him fast.  You'll take damage, but try to spin again.  You may be able to defeat him in one assault if you time it well.  If, for some crazy reason, the Top Spin empties on you, the Search Snake is also effective.  Once Wily's ejected from Gamma, you've done it!  Congrats!

Weapon Notes
Search Snake
You can fire 2 Search Snakes at a time.  They will proceed to quickly crawl along the floor and can also scale walls.  They disappear when they reach the ceiling.  They are fairly heavy, making them fall to the floor like rocks when shot.

Spark Shock
The Spark Shock can be fired one at a time at a fairly quick pace.  It has the handy ability to stun normal enemies, but it also restricts your ability to pause to switch weapons or to fire additional shocks while the enemy is stunned.

Gemini Laser
The Gemini Laser can be fired one at a time.  It can bounce off of the stage's walls and ceilings until it strikes an enemy or breaks apart after a few bounces.  It is very slow, so use it cautiously.

Needle Cannon
The Needle Cannon is a rapid-fire Mega Buster, in my opinion.  It shoots out Needles three at a time at a very fast clip.  However, it drains the meter faster than any other weapon in the game (outside of the quirky Top Spin).

Magnet Missile
Magnet Missiles can be fired two at a time.  They home in on enemies by changing direction once, either upwards or downwards, when they cross its path.  Because of that, sometimes you can easily burn Magnet Missile ammo unintentionally on enemies that move quickly.

Shadow Blade
Two Shadow Blades can be flung at a time.  They can be thrown in three directions - straight ahead, straight above, or at a diagonal slant.  The only downside is their somewhat short range.

Hard Knuckle
The Hard Knuckle can be fired one at a time.  This powerful Knuckle can be steered slightly after firing it by pressing up and down.  It can also destroy barriers in Wily's Castle that other weapons can not.  It is very slow, though.

Top Spin
The Top Spin can only be performed when Mega Man is in the air.  Press the fire button and Mega Man will spin.  This tears a lot of normal enemies apart with one strike.  However, Mega Man usually trades hits with his enemies performing this move (some will just explode with no consequence), and it also has a nasty habit of draining a ton of its weapon meter randomly.

Secrets
* Need some Energy Tanks?  Go to the password screen and put a red dot on A6.  When you start, you'll have 9 energy tanks in your inventory, the maximum you can carry!
* If you have a second controller, you can perform two special cheats, one that (with some effort) can make you invincible for the duration of the stage! (Note - this was removed from the PS2/GC/Xbox Mega Man Anniversary Collection, but the Virtual Console version works the same as its NES counterpart).
- Hold up to make the game's sprites slow down.  The animation will be heavily reduced, to the point that they're hardly moving.  This slows down attacks a bit as well, and increases Mega Man's invulnerable phase when he's hit.  However, it also slows down Mega Man's bullets, so he won't fire as fast as he normally could.
- Hold right to unleash Super Jumps, which make Mega Man leap like he used the Rush Coil (and then some)!  However, this trick also can let you survive falling into pits, as long as you tap it before a certain point.  You must hold the direction to remain safe in pits.
* Using the Super Jump trick, you can "fool" the game into making you invincible!  Fall into a pit and hold right.  Walk Mega Man under enemies above you, and he'll usually take damage.  When the life meter depletes, he won't explode like he usually would, since the game considers Mega Man dead for being in the pit already.  Leap out and you'll find that enemies can still strike you, but it will not kill you!  There are four drawbacks to this, though:
1) Spikes will still kill you, as will pits (if you fail to use or hold the Super Jump)
2) The Mega Buster will not work anymore.  You'll need to switch to a Rush Adapter to fire standard shots (the Rush Marine works best for this, although the drawback is you can only fire two bullets instead of three at a time).  Your Robot Master weaponry will still work, though.
3) Picking up a life capsule or using an Energy Tank will render your invincibility null, as it will refill your life meter and undo the cheat.
4) The stage music stops...which is a shame, since the music is so good!
* In Snake Man's stage, if you are unsatisfied with the results of the ? Tanks, you can reset them by climbing back down the ladder and heading back up.  The tanks will be restored, and you can fire on them until you get 1-Ups or Energy Tanks.

Passwords
(Note - C5 Red stands for no energy tanks, so you can replace it with A6 Red to get 9 reserve tanks!)
Top Man (alone) - A3 Red, C5 Red
Shadow Man (alone) - D6 Red, C5 Red
Magnet Man (alone) - F5 Red, C5 Red
Needle Man (alone) - D3 Red, C5 Red
Hard Man (alone) - C4 Red, C5 Red
Gemini Man (alone) - B5 Red, C5 Red
Spark Man (alone) - F4 Red, C5 Red
Snake Man (alone) - F6 Red, C5 Red
Dr. Robot (all 8 Masters defeated) - A3 Blue (Top Man and Snake Man), B5 Blue (Gemini Man and Hard Man), D3 Blue (Needle Man and Magnet Man), F4 Blue (Spark Man and Shadow Man), C5 Red
(Note - If, for some reason, you want to take down only a few bosses at a time, I've noted what the blue dots signify in terms of what bosses they are.  So, if you wanted to have the Needle Cannon, Magnet Missiles and Search Snake at first, you would put down F6 Red for Snake Man, and D3 Blue for Magnet Man and Needle Man.  Putting the red dots for bosses that cross like this will not work!)
Break Man (all Dr. Robot stages completed) - A1 Blue, A3 Blue, B2 Blue, B5 Blue, C5 Red, D3 Blue, F4 Blue
Dr. Wily's Castle - A1 Blue, A3 Blue, B2 Blue, B5 Blue, C5 Red, D3 Blue, E1 Red, F4 Blue
(Note - There are no passwords beyond Stage 1 of Wily's Castle, so you'll have to march through the whole thing)

Most of the art for this feature came from The Mega Man Network.  Thanks!