Mega Man 2 Walkthrough

This is a walkthrough for Mega Man 2 from NES.

Level Strategies: Robot Masters
Although it is possible to complete the eight main levels in any order, this walkthrough provides a recommended order that will make defeating bosses and some enemies easier. However, there is no need to follow the order given, and each level strategy can be read alone.


 * Suggested order:
 * 1) Air Man: he suffers double damage from the regular Arm Cannon; moreover, when defeated he also drops the Item-2, extremely useful in later Heat Man's stage;
 * 2) Crash Man: he's weak against Air Man's A. Shooter;
 * 3) Flash Man: he's weak against Crash Man's C. Bomber;
 * 4) Quick Man: he's weak against Flash Man's Time Stopper and Crash Man's C. Bomber;
 * 5) Metal Man: he's weak against Quick Man's Q. Boomerang;
 * 6) Bubble Man: he's weak against Metal Man's M. Blade;
 * 7) Heat Man: he's weak against Bubble Man's B. Lead; his stage can be very difficult without Air Man's Item-2;
 * 8) Wood Man: he's weak against Heat Man's Atomic Fire.

Air Man (Sky Ridge)

 * It is recommended to use Leaf Shield to Defeat Air Man.

This level is entirely made up of floating platforms over pits, so if you're not good at jumping, you can always use Item 1 to make the trickier jumps. As you approach the end of the platform you start on, an Air Tikki (large head) will materialize. This is your platform to cross, but don't jump on it right away, because it slowly raises (non-lethal) spikes on both sides of its head. Wait until the spikes drop and jump across to the next platform. You will have to jump across five of these Air Tikkis in this area. They also send out Gremlins (small heads) that swarm you, so watch out for those and take them out if necessary. After this, a Lightening Lord (an enemy on a cloud) will approach you, throwing lightning. You will have to kill him and ride his Cloud Chariot. There are five of these and you will have to use all five clouds. The third one is tricky to kill: you must jump to fire at him or aim Metal-Blade diagonally in order to kill him in time to jump onto his cloud. For the fourth one, wait until he is behind you or aim Metal-Blade up. Once you're back on solid ground, just run along and watch out for the Pipi. Some of them are behind clouds, so be careful. Once you reach the very edge of the screen, you will drop down behind a cloud to the next screen.

Ignore the Boomerang Blowers in this room and drop down behind the cloud on the left side. (Don't worry, there are no more pits hidden behind clouds.) Once again, an Air Tikki will appear, and another one will appear once you are at the edge of the first one. Unfortunately, this means that it will be hard to jump to the second one, as it will have spikes up when the first has spikes down. Item 1 lets you avoid this tricky jump. Next comes a platform with a Fan Fiend (fan creature) on it. This enemy will blow you back, so keep jumping forward as you shoot it. Take out all the Fan Fiends in this area and watch out for more Pippis.

Air Man uses Air Shooter, where he shoots out a bunch of mini-tornadoes and then blows them towards you. He will do this three times, then jump across the stage and start firing them the other way. Jump and dodge the tornadoes as best you can, but there will probably be some that you cannot dodge. The tornadoes deflect your shots, so wait until he is jumping to fire. The Leaf Shield will kill him quickly, and you get the Air Shooter and Item-2, a incredibly fast hoverboard, for clearing this level.

Crash Man (Bombing Facility)
This level is one big tower with a lot of ladders. Climb up the ladders at the beginning, ignoring the Tellys (cylinder enemies). You can kill them easily with Metal-Blade if you feel the need. Once you reach the top of the ladder, kill the Mets and proceed upward. Here you will see a moving platform on a square track. Ride it to the ladder at the top, avoiding or killing the Tellys. The Leaf Shield is very useful here, since you are not technically moving when on the platform, so the shield will protect you for the entire ride. Climb up and repeat the process on two more platforms on tracks, this time with more complicated shapes. When you reach the top, kill the Blocky here and climb up two screens. To kill the Met, jump onto the platform to your left, then quickly jump back. The Met will move to the next platform, where it is easier to kill him. Jump across and climb the ladder.

Here you will see two ladders, and once you climb onto the next screen they branch off into five ladders. The first and third lead to dead ends, the second leads to an energy tank, the fourth leads to a large energy capsule, and the fifth is the path that leads to the top. So take the rightmost path, watching out for Pippis. The best way to deal with them is to hold still when they appear and use the Leaf Shield when they drop the eggs. Notice that when you climb the branching ladders, the background darkens as you're climbing above the earth! Once at the top, if you have Item 1 or 2 you can drop down and get the energy tank, then use the item to get back up. Here are another two ladders, the left of which requires Item 1 or 2 to reach. If you have one of the items, take the left ladder for a 1up. In the final room, avoid the Prop-Tops (enemies that fall and chase you), or kill them with Metal-Blade.

Crash Man jumps around the stage throwing bombs at the walls and floor. Run under him and dodge his bombs, and shoot him at any time. He always jumps when you shoot, so you must jump and shoot him in the air. He is weak to the Air Shooter, that shoots upwards, and since Crash Man jumps whenever Mega Man shoots, he's the ideal target for the Air Shooter. Your reward is the Crash Bomber, which can be used to break open certain walls.

Flash Man (Crystal Caves)
The floor is slick in this level, so you will slide for a bit after stopping, and will have to pick up speed when you start to move again. The level quickly branches off into three paths. Do not take the top one because it leads nowhere. The middle path has a large energy capsule, but you will probably not need it. The bottom two paths have Crazy Cannon (round enemies that shoot pellets at you); they are easy to dodge and kill. After this there is a high ledge with a 1up on it. You can use Item-1 to reach it, or take the lower path if you don't have that item. The next high ledge also requires Item 1, and has short walls blocking the way. If you have the Item-2 instead, it can still be done, although it's a bit tricky. These walls can be broken by the Crash Bomber. If you do not have these items, pass another Crazy Cannon and drop down to the next area.

On the left side of this screen is a Robot Walker Joe; the right side simply drops down. You can again choose which side to drop down into; the right side is preferable. The next screen has a large energy capsule behind a crash wall, accessible only from the right side. Drop down again and destroy the enemies, then drop again. If you are on the right side, drop close to the left wall and hold left, and you can land on the platform above the Robot Walker Joe. There is a large energy capsule here, but getting it means having to kill the Robot Walker Joe. Air Shooter is effective against them. Drop down the right side and you will come out on a high platform. Jump across the small platforms here to reach an energy tank. Even if you have Crash Bombs, don't break the wall; instead, go back and defeat the last Mech Joe to get to the central mining room, which is the boss room.

Flash Man jumps around the stage for a few seconds, then he will freeze you in your tracks and fire pellets at you. It is not hard to dodge him when he is moving, but to avoid his shots you'll have to time it so you are out of his range when he freezes you. He is weak to Crash Bombers, and defeating him gives you Time Stopper and Item-3, a wall-crawling platform.

Mission Complete: The Crystal Caves have regained time, and Flash Man is destroyed.

Quick Man (Underground Factory)

 * It is STRONGLY recommended that you have the Time Stopper before attempting this level.

Use Item-1 or Item-3 to get the 1up on your left, then drop down, pass the Scworm (worm-squeezing enemies) and drop again. The next three screens have fast moving laser beams that spell instant death. Fall through the area as quickly as possible to avoid them. If you fall onto the right side of the screen, your reward will be a 1up, energy tank, and large weapon capsule. Drop down again and into darkness. There are Hothead (flamethrower enemies) here that illuminate the room. Killing them bring you into total darkness, but is necessary to continue. When in the darkness, keep jumping as you go, for the terrain is uneven. The room will light up again as you reach the end. Here it is once again recommended that you use the Time Stopper before dropping into the particle beam's main turret.

What follows is seven screens of more lasers, with platforms strategically placed to give you just enough time to get through. It is exceedingly difficult unless you use the Time Stopper. The third screen has a large energy capsule that you can use to refill your Time Stopper, but it will still run out by the last two screens. Do not get the health capsule or 1up on the fifth screen, or the weapon capsule on the seventh, as there is not enough time. Quickly dodge the last few lasers once your Time Stopper runs out and drop into the final area. Defeat the two Robot Walker Joes here to reach the control room.

Quick Man will jump very high around the room and shoots sets of three boomerangs at you. Run underneath him when he jumps and jump over his boomerangs. He is weak to the Time Stopper (the full Time Stopper will take away about half of his health) and Crash Bombers, and gives you the Quick Boomerang when you defeat him.

Metal Man (Lost Factory)
The first thing you will notice about this level is the conveyor belts moving the ground. Some parts move forward and increase your running speed, some move backward and slow you down. Go forward, go onto the lower platform, get the Energy Tank and go back onto the upper platform. Here you will have to pass a series of spiked clamps, Press. They cause high damage when you touch them, so let them drop and move under when they are going back up. After passing them, you will enter a tunnel in which Moles (screws) appear from the floor and ceiling. They are not hard to dodge, and killing them often yields large capsules, so kill a bunch if you need health or weapon energy. The last part of the tunnel has a moving ground, which makes dodging the Moles a bit harder, but just don't go forward too fast and you'll be fine. After this, jump across the platforms, and if you have Item 1 or 2 you can get the 1up on the high ledge. Drop down onto the next screen, which has no enemies, and drop again.

Move forward and you will see a gear hanging in the air. When you approach, a Pierobot (the little clown) will drop onto it and ride it towards you. The gear keeps moving if you kill the Pierobot, so destroy the gear instead, and the Pierobot will fall. Make your way across the platforms destroying the remaining gears. Next are two Blockys (enemies that look like four cans stacked on top of each other). Shoot them in the face to kill them. Dodge the cans if you are playing in Difficult Mode. If you have Item 1 or 2, drop down to get the Energy Tank and use your item to cross. If not, you can just make the jump from the top ledge. Pass the Spring Heads (spring enemies) (Quick-Boomerang is useful on them) and enter the boss room.

Metal Man stays on the opposite side of the room as you (so he will only move from his place if you approach) and shoots Metal-Blades. Jump over the blades and shoot, and watch for the change in the direction that the floor moves. Metal Man is weak against the Quick-Boomerang, and defeating him gives you the Metal-Blade.

Mission Complete: Lost Factory is secure and Metal Man is destroyed.

Bubble Man (Waterfall Institute)
You start out on a platform over a pit. Make your way across several floating platforms, killing the Croakers (frogs) that get in your way. It's tricky to kill the Mini Croakers (baby frogs) with the Mega Buster, so try Metal-Blade or the Leaf Shield. Soon you will come across a series of small platforms that look like crash walls on their sides. These drop away almost as soon as you touch them, so jump over them quickly, or use Time-Stop to prevent them from falling. Try to jump to the far side of the first one so you don't have to run across before jumping again. Once you're back on solid ground, drop down, kill the Crabbots (hermit crabs), and drop two more times into the water. Try to fall on the right side so that you avoid falling on another Crabbot. Kill these and drop down again.

This entire area has a ceiling lined with deadly spikes. Remember, you can jump much higher underwater, so be careful. A Lantern Fish (giant anglerfish) that shoots out Squirts (shrimp) is your first obstacle. Shoot the light dangling from its head to kill it. Next you will need to do some controlled jumping around uneven terrain, avoiding the spikes. Use Metal-Blade to kill the M-445s (jellyfish enemies that descend on you), as it can shoot up. Another Lantern Fish is next, followed by two more Croakers. Once you pass them, you will come out of the water and make your way across a few floating platforms. Snappers (crabs) will descend from the sky, so wait until they fall or use the Time Stopper to avoid them, and enter the boss room.

Bubble Man will use Bubble Lead, where he shoots out 1-3 bubbles, then swim diagonally up while shooting at you, then swim down to repeat the process. The bubbles are not hard to dodge, since you can jump high, but be careful of the spikes on the ceiling. The best time to hit him is when he is swimming down, as he does not fire at you then. He is weak against the Metal-Blade, and defeating him gives you Bubble Lead.

Heat Man (Heat Furnace)

 * It is recommended that you have Item-2 before attempting this level.

Jump over the lava pits, avoiding the Prop-Tops. Avoid the Tellys or take them out with Metal-Blade, then jump across the platforms and dodge the spring enemies or use Quick-Boomerang on them. Climb down into the next screen. There are Yoku Blocks (disappearing blocks) here. Jump onto the first one as soon as it appears, then immediately jump straight up and you will land on the next block. Jump across the remaining blocks to the ladder. You can use Item-3 on the far wall to bypass this puzzle.

Next is a long area where you will have to jump onto Yoku Blocks to get over walls, all while avoiding Tellys. Metal-Blade is extremely useful for getting them out of your way. Jump across the blocks, and make note of instances where you have to jump again to land on a block above the one you are on. Many of the walls are breakable with Crash Bombs, so use them if you have them to bypass the jupming. After this, run along and jump onto the upper platform. What follows is a very long section of disappearing blocks you have to cross, making sure you do not fall into the lava flow or pit. Some of the blocks have blocks appear right above them, and this spells death if you do not jump up in time. This is where Item 2 comes in. You can use the item to cross the entire area without fear. You can also jump down to get the 1up on the ledge if you think you can make it. If you do, be sure to wait until the blocks on the lower right disappear before casting Item 2 again. Once you reach the end, climb down the ladder and take out the Robot Walker Joe (Air Shooter is good for this). Climb down to the volcano's core and into the base's control room, which is the boss room.

Heat Man uses Atomic Fire, where he tosses three flames at you, which form pillars of fire once they hit the ground. When you hit him, he will use Bodily Crash, where he will stop, raise a heat shield for a second, then streak across the room as a comet of fire. Jump over him when he is crossing the room and heep hitting him to prevent his flame attack. DO NOT use Crash Bomb! It refills his health! He is weak to the Bubble Lead, and killing him gets you the Atomic Fire and Item-1, a hovering platform.

Wood Man (Forest Base)
This level is much easier if you simply equip Metal-Blade at the beginning and use it for the entire level. The first room is easy; the Bubble Bats (bats) in the trees are slow and weak, and the Robo-Rabbit do not pose much threat either, although they will shoot out carrots. Climb down the ladder, past some more Bubble Bat, and down again. Here you will face a Hot Dog (a large blue wolf-like creature). Jump over his fireballs and shoot him; he is not hard to kill. The next two rooms also contain Hot Dogs. If you want to avoid them, use the Time Stopper in the room before the first one and they will not appear. Climb up the ladder, past the Bubble Bats, and up again.

This room will have Pippis (birds) flying across dropping eggs, which hatch into many Feathers (baby birds). It is easier to use Metal-Blade to eliminate the egg before it hatches, but the Feathers give out lots of large capsules if you kill them. On most of the platforms here, Mecha Monkeys jump up and hang on to the platform from beneath. You can kill them by shooting the Metal-Blade diagonally downwards, or approach them to make them jump up. Climb down the ladder and kill the Robo-Rabbits in the next three rooms, climbing down into the final room. Your only enemies here are Atomic Chickens that jump every few steps. Kill them quickly or run under them when they jump.

Wood Man uses Leaf Shield and Leaf Fall together, where he forms a shield of leaves around himself, shoots four leaves up, then tosses his shield at you as the four leaves descend. You can only hit him when his shield is down, so jump over it when he tosses it and fire away. He is weak to Atomic Fire, but it should be noted that it only does much damage to him when it is fully charged, so charge it while his shield is up (he can be defeated in one fully charged hit on normal, and two on difficult). Barring that, the Air Shooter does decent damage, and the blast radius of the Crash Bomber can hit him even while the shield is up. You get the Leaf Shield for defeating him.

Wily 1: Castle Grounds
First you will pass through a large open area with Pippis dropping eggs. Use Metal-Blades to kill them. You will soon come to a wall. Use Item 1 or 3 to get up. I recommend Item 3 because you will be needing Item 1 later on. The Leaf Shield is helpful against the Boomerang Blowers past the wall; just keep running and casting it. Use Item 3 on another wall and pass another Boomerang Blower. Item 3 up the wall to your right. If you want, you can pass the Boomerang Blower on the ledge for the 1up, but you will need to climb the wall again if you do. Climb the ladder and pass the Sniper Joe. You can pick up the large weapon capsule if you need it. Climb the next ladder, pass another Sniper Joe and climb another ladder to reach an open screen with a Spring Head. Pass it and climb the ladder, you will find yourself on a screen with a ladder in the far corner. Stand on top of the ladder you just climbed, cast Item 1, and jump on it. Cast another and jump on it, and cast a third time to reach the ladder. Climb up two screens, ignoring the Tellys, and continue onwards at the top. Jump across the platforms, and soon the level will start to move. The Mecha Dragon will appear behind you with a screech and knock the blocks away. Let him chase you until you reach an areas with three uneven platforms, then prepare to fight him.

The Mecha Dragon will move up and down, shooting either one fireball or a stream of fireballs at you. The hardest part of this fight is staying on the platforms, as the fireballs knock you back quite a distance. Try to stay on the leftmost edge of the platform and jump over his single fireballs. Jump to another platform when he uses his stream attack. The dragon is weak to Quick-Boomerangs.

Wily 2: Transfer Circuit
Get the large weapon capsule if you need it and proceed, taking care to avoid the Prop-Tops. Get the second weapon capsule and cast Item-2 at the edge of the platform to cross the spikes. Pass the first ladder, jump onto the second one and get your energy tank. Climb down and fill whatever you like with the nine small weapon capsules here. Climb down and use Crash Bombs on the walls to get your 1up and energy tank, taking care to avoid the shots coming from the other side. Drop down and avoid the spikes, and drop down again.

Pass through the narrow tunnel here, in which the Moles from Metal Man's stage reappear. You can use Time Stopper to avoid fighting them, but they're not that difficult. Use Item-3 to get up the wall at the end of the tunnel, and be careful not to touch the clamps. The last two clamps have just enough room for you to squeeze between. If you didn't use Time Stopper on the screws, you might want to use it now. Drop down, avoiding the spikes (pausing the game is useful here.). Use Item 2 to get the large energy capsule if you need it, then drop into the central computer station, which is the boss room.

The boss is the Picopico-Master (the blocks that make up the walls of this room). Two of them will break off, join together, transform, and fly at you progressively faster as the you destroy them. Your best bet is to use Metal Blade to aim at them before they can reach you. Watch out for Picopico-Masters that come out of the floor, and stay near the middle of the room to avoid getting hit when one pops out of the wall. There are fifteen of the robots in all. Don't be afraid to use lots of Metal Blades; the blocks do a good amount of damage if they come in contact.

Wily 3: Waterway Defense
Drop down on the right side to land on a ledge. You can break the walls here with Crash Bombs for an energy tank and large weapon capsule; however, I recommend conserving your Crash Bomb supply. If you go onto the lower platform and drop to the right, you will be able to get two more large weapon capsules. Ignore the Crabbots and crop down into the water. Jump across the platforms here, avoiding the spikes. The larger pits have Big Fish (fish) that jump up at you, so jump to the maximum height to avoid them. Jump down between the spikes, and get ready for some tricky controlled falling. You'll need to tap to the left a bit to dodge the spikes as you fall down four screens of them. When you reach the ledge, drop down to the bottom of the screen, making sure to drop on the right side to avoid the spikes on the last drop. Jump out of the water and proceed, killing the Crazy Cannon, until you reach the defence station, which is the boss room.

The boss is Guts-Dozer (a large tank in the likeness of Guts Man). It moves back and forth slowly, firing shots out of its mouth and sending out Mets. Jump onto the flat part of the tank and shoot it in the head, dodging the Mets and his hand. This boss is weak to the Quick-Boomerang.

Wily 4: Security Station

 * Note: You MUST have Crash Bombs at 100% in order to defeat the boss of this level, so don't waste them. You will also need at least 25% of all three items.

Fill the Crash Bomber with the two large capsules at the beginning (they restore more them what is used). Climb up and kill the Met, and climb up to the top of the ladder on the next screen. There is a Met on a ledge below you, and there is an invisible hole in the floor right above where the Met sits. You can use Bubble Lead to determine exactly where the invisible holes are. If you need a 1up, drop down through the hole, kill the Met, and use Item-1 or 3 to get back up. Climb down the ladder for your 1-Up, then climb it all the way to the top. Avoid another hole here, climb onto the ledge, and jump over two more holes to the ladder. Climb onto the next screen and cross the spikes. There is a hole just before the ladder; use Bubble Lead to find it and jump or just use Item 2 to cross. Climb again into a room with three ledges. The top one has an energy tank, but there is a hole in front of it, right above the met below. Drop down, kill the Met, and use Item-1 to reach the tank. Climb again and run along until you come to another ladder. Climb down it, but don't let go and jump down, for there are spikes below.

Hang onto the ladder and wait for the platform to reach you. The Leaf Shield is your best bet to protect you against the Tellys. Ride the platform until you reach the ladder going down and climb down. Hang onto the ladder until the platform reaches you, and ride it until you ride under a small ledge. Jump onto the ledge, for the platform will go through a passage that you can't fit through. Jump back onto the platform and ride it to the top, then climb down the ladder. Once again hang on until the platform reaches you and use Leaf Shield on the Tellys. Jump over the ledge in your way as you ride this platform down. Drop onto a large ledge on the next screen and wait on the edge for the platform. When it reaches the bottom right corner of its path, jump onto it and then immediately jump to the small ledge in the air. Use Item-2 to cross to the next ladder and climb down. Kill the Sniper Joes and mech Joes in the final room and head into the main security center, which is the boss room.

This boss, named the Buebeam Trap, consists of 5 round Sentinels attached to the walls, in a room filled with ledges and Crash Bomb walls. They never move, and will flash red before firing at you in unison. They can only be killed by the Crash Bombs, and you will need to use all seven shots to clear this stage. This boss is more of a puzzle than a fight, and it will take skill and precision to defeat. Before taking on the fight, look at each of the Sentinels and how they are placed. You will have exactly enough Crash Bomb to defeat all necessary walls and all the Sentinels. Look to see which walls are necessary (the Sentinel is fully guarded by them) and which ones aren't (the walls can be bypassed using Items 1 or 3) First, use Item 1 to reach the ledge in the center of the room. Jump up to your right and kill the Sentinel there, then jump back down to the central ledge. Drop to your right and break the two walls to your right, then kill the Sentinels behind them. Use Item 1 or 3 to get back up to the central ledge. This is the trickiest part: Move to the left edge of that ledge and jump up onto the ledge above, but don't kill the Sentinel there. Drop off of that ledge, and as you fall, fire a Crash Bomb at the space in the wall between the Sentinel and the Crash wall below it. The resulting explosion will destroy both the Sentinel and the wall. Use Item 1 to get back up and kill the last Sentinel with your last shot. Should you miss even once, stop firing and allow the Sentinels to kill you. Refill your Crash Bombs in the level and try again. You will find that any walls you eliminated before you died will not return (however, the Sentinels will).

A second method is to enter the room and only attack and destroy all of the walls. Do not attack any of the Sentinels as it is only a waste of energy and time, both here and later. After the walls are destroyed, purposefully die. Once back out in the level, take the time to gather energy and refill the Crash Bomb weapon. Once it is full, re-enter the boss room and destroy the Sentinels, as they will no longer be guarded by any walls. Keep in mind that this method, obviously, requires you to have more than one life. If you use a continue, the walls will return.

Wily 5: Teleport System
This is not a level, but merely a room with eight teleport hatches in it, called Wily Teleport System. Each hatch will teleport you to a room in cyberspace where you will have a rematch with one of the Robot Masters. The hatches are laid out as follows:

Take them out in any order you like. The fights will be exactly the same as the last time, so the same tactics will work (remember that Metal Man is weak against his own weapon!) Anyway, don't use the following weapons:
 * Crash Bomber: mostly used up against the previous boss, and if any is left, save it for the second Wily Machine; use Metal Blades against Flash Man instead, and against Quick Man use your Arm Cannon after the Time Stopper;
 * Atomic Fire: necessary against the first Wily Machine; use Air Shooter against Wood Man instead;
 * Bubble Lead: necessary against the final boss; use the Quick Boomerang or the Arm Cannon against Heat Man instead.

When you defeat a Robot Master, he drops a large energy capsule. After you defeat all eight, a ninth hatch will appear that leads to the fight with Wily. Dr. Wily rides in his UFO attached to a spaceship and fires large energy blasts at you as he moves back and forth. In his first phase he shoots balls of energy that move down, then arc back up towards you. Stay close to the left side of the screen and jump over the balls before they get too high. Jump and fire two fully-charged Atomic Fires at the front of the ship.

Once you deplete his energy this way, part of the ship breaks away to reveal Wily's face, and the second phase begins. He continues to move back and forth and shoot balls, but this time they bounce along the floor. It is very difficult to dodge the bouncing shots, but watch the patterns and try to jump over them when they are at their lowest point. Wily's weakness in this phase is the Crash Bomb, and it will take him out pretty quickly. If you run out of them, switch to the Metal Blade. Once you defeat him, the final stage will appear on the map.

Wily 6: Fortress Caverns

 * Note: You must have an adequate supply (about 50%) of Bubble Lead in order to defeat this boss. If you don't have enough, your best bet is to die on purpose, then choose 'Continue' on the Game Over screen.

First you will drop three screens. Don't worry, there's nothing there to hurt you. Once you land, you will have to make your way through a cave in which acid drips from the ceiling. This is the only enemy here, but it does high damage, so avoid it at all costs. The acid drips at regular intervals, so watch and wait for the right moment to pass under. Time Stopper will of course make your progress much easier, but don't use it when the acid is in mid-drip or you will have wasted it. At the end of the cave lies the final boss: Alien.

You will find yourself in a dark, featureless room. Wily will appear before you and transform into an alien. Then stars appear in the room, and the battle begins. He will fly around the room in a figure eight pattern and shoot buster shots at you. The only weapon that will damage him in this form is Bubble Lead. Warning: do NOT attempt to use any other weapon on him, including your plasma shot: it will actually refill all of his energy! Wait until he flies to the bottom of the screen, then jump and hit him with your bubbles. You can get several hits in at once if you are fast enough. He has no "invulnerability" period after being hit, so the faster you shoot, the more damage you do. His shots are weak, but touching him will take away nearly half your health, so be very careful when jumping. Watch his pattern and make sure you are not under him when he descends. Simply repeat this process until you defeat him. You will see that Wily is just a hologram. The Alien is a flying ball. Enjoy the ending.