- In Order of Appearance
 Ridley (Prologue)
Encountered whilst stealing the Baby Metroid from Ceres. A short battle that features Ridley shooting fireballs and charging at Samus. The battle ends when Samus's health falls below 30 or Ridley takes enough damage, whichever happens first.
After grabbing the Morph Ball Bombs, the door will close. The statue will stand up and start walking toward Samus. Rolling into a ball is a good defensive tactic here, especially to dodge its crescent beam blasts and to roll back from its arm attack.
The projectiles that Torizo shoot from its mouth can be shot, which will sometimes drop Energy and Missile ammo. Firing Missiles into its abdomen will do the most damage but the creature is vulnerable to Power Beam attacks as well.
 Spore Spawn
Spore Spawn is a mollusk-like plant that moves around in a figure-8 pattern. As if using Morph Ball to avoid getting rammed by its movement pattern were any challenge, spores drop from the ceiling as well, which can hurt Samus but also drop Energy and Missile ammo.
When Spore Spawn opens its shell, fire Missiles or Charge Beam blasts into it to cause damage. As it takes damage it darkens in color and will move faster. Once defeated a hole opens in the top of the ceiling, and the plant-life in the room decays in color.
Kraid will rise up from the spike-covered floor to start the battle. It'll shoot rocks at Samus if it opens its mouth without provocation, so the best way to dodge that is to shoot Kraid in the head to draw its mouth open, then fire away with Super Missiles for the most damage.
Once it takes enough Damage, Kraid will rise completely out of the ground, and start shooting spikes at Samus from three sections on its torso. These can be used as platforms to get to the upper ledges if the Hi-Jump Boots weren't acquired ahead of time; alternatively the Wall-Jump can also be used to reach said ledges. Four Super Missiles will finish Kraid off, but Missiles and Charge Beam can be used if Samus runs out.
Crocomire is a very tough customer, and the only thing that will take it out is the fiery lava of Norfair itself. At one end of the room is a wall of spikes, which will finish Samus off; at the other end a walkway over a pit of molten magma.
A general rule-of-thumb: every time Crocomire opens its mouth a Super Missile or Charge Beam shot should be fired into it. Missiles don't push Crocomire back too far, and in addition to slowly trying to push Samus back it'll sometimes stop and fire projectiles, which can be shot for Energy and ammunition. Once in the pit of magma Crocomire dissolves, then eventually reappears at the other end of the room as its skeleton, breaking the wall but falling apart.
An Energy Tank is at the other end of the magma pit, which requires a good Wall-Jump or the Grapple Beam to access.
So far, the bosses haven't been terribly difficult. That ends here, with the boss of the Wrecked Ship, Phantoon. In addition to being subjected to fireball RNG (random number generation), when the boss reveals its weak spot is also subject to RNG.
Phantoon's weak spot is its eye, and Super Missiles, while they do a lot of damage, will also draw Phantoon's rage, as it'll retaliate with multiple fireball rounds from the top of the screen! This also takes time per hit; when trying to beat the game in under 3 hours this can be a trouble spot.
The fireballs can be shot for Energy and Ammunition, but they can also interfere when trying to hit Phantoon when its eye is exposed. Varying strategies for this boss exist, from using Missiles to Charge Beam as a means of avoiding losing time to Phantoon's fireball barrages.
A popular and widely used strategy by speedrunners is the "X-Factor" strategy (unofficial name). This involves using the Charge Beam Combo for the Wave Beam and Power Bombs (Ice and Spazer Beams are turned off for this). After shooting Phantoon with a Missile, quickly switch over to Power Bombs and charge the Charge Beam with only the Wave Beam activated to launch "X-Factor," such named for the four Wave-Beam blasts that cross at the center of the screen, then they home in on their targets for major damage!
Botwoon's weak point is its head, which can be blasted with Super Missiles as it moves about its room. The only real dangers here, other than getting rammed by Botwoon (especially when it speeds up after it takes damage) are the green projectiles that it fires.
Draygon is a crayfish boss that has two different strategies for defeating. Either way, blast the turrets that are on the walls with Super Missiles to render them inoperable. The battle begins after the mini-Draygon's leave.
Draygon sways from side-to-side as a means of attacking. Getting hit by this hurts, even with both the Varia and Gravity Suits activated, and as it speeds up from taking damage this becomes tougher and tougher to avoid. During these passes its stomach region is vulnerable to being hit with Super Missiles. Avoid its spit at all costs, especially if you're low on health. If the spit hits you Draygon will grab Samus, leaving her very vulnerable to damage and Charge Beam combos as the only means of doing damage. As Draygon is holding onto Samus it'll attack her with its barbed tail, damage that will add up in a hurry.
Or, if you're trying to defeat Draygon with relative ease, you'll want Samus to get hit by its spit. With the turrets destroyed they leave behind a point that can be accessed by the Grapple Beam, one that would hurt Samus should she ever shoot that point with the Grapple Beam. Should Samus shoot this point while Draygon is holding onto Samus, the electric current will arc through Samus into Draygon, quickly finishing the boss of Maridia off.
 Golden Torizo
Torizo was just a warm-up compared to its lower Norfair counterpart! Its attack patterns, albeit similar to Torizo, are faster in intensity and also include eggs that hatch birds and an eye-laser! Golden Torizo will sidestep regular Missiles, and forget about Super Missiles--it'll catch them and throw them back at the sender! A charged Plasma Beam works best here, use Space Jump to avoid the Crescent-Beams and some of its other aforementioned attacks.
At any time during or after the battle, set off a Power Bomb in the top-right corner of the room to reveal an alcove where a Super Missile expansion rests.
 Metal Space Pirates
Ridley's personal bodyguards are the toughest Space Pirates you'll face in the game. No attacks will damage them...at first. The trick is to avoid their projectile attacks (don't get too close or else they'll attack by kicking!) and let them jump over Samus. Then, when they turn gold, they're vulnerable to attack, Super Missiles or charged Plasma Beam will do the trick.
Defeating both will unlock the Metal Door on the left-hand side of the room.
 Ridley: Norfair
In a tall room, situated with one platform in its middle, is where Samus encounters Ridley for the second time in the game. In addition to attacking with fireballs, Ridley will also employ its tail to strike at Samus.
This battle's all guns-blazing, and everything does damage to Ridley, including Power Bombs, Super Missiles and Charge Beam attacks. The one spot in which Ridley won't take damage is its tail.
There's an exploitable glitch in this battle where Ridley will die should it grab Samus while it's low on health. In the room to the left is a hidden Energy Tank below that room's lone door.
 Mother Brain Form 1
First things first, the Zebetites need to be destroyed in order to reach Mother Brain, and like it was in the original Metroid there are four. These will be destroyed with a Missile barrage, and to make matters worse they'll regenerate if they don't take constant damage, so unless you're trying to beat the game on minimum energy (3 Energy Tanks) don't worry about taking hits.
Once Samus reaches Mother Brain's tank, a barrage of Missiles will eventually open a hole in the glass tank. After it's opened fire Super Missiles to destroy Mother Brain's life-support systems.
 Mother Brain Form 2
But it's not over yet. The brain lifts up to reveal a massive battle-body unlike any seen before it! The weak spot remains the brain--that hasn't changed.
It's the offensive arsenal of Mother Brain that has changed the most! She'll shoot a beam from her eye, along with ring lasers from her mouth and occasionally dropping bombs from her mouth as well. Jumping is the best method for dodging the ring lasers and bomb blasts, but if you jump too often the Brain will shoot its eye beam.
After taking enough damage Mother Brain will stop moving around and try to blast Samus with a red energy beam, which does a lot of damage in its own right. After further damage, Mother Brain will fire an energy-draining beam that'll do 300 Damage to Samus per hit! Eventually, Samus will become too weak to fight back and a cutscene will play out once Samus falls below 100 Energy.
The cutscene has the Baby Metroid, now grown to ginormous proportions due to exposure to Beta-Rays, drain the energy out of Mother Brain and transferred to Samus. Mother Brain regains its energy and kills the Baby Metroid as a result of its betrayal, but Samus gains the Hyper Beam as a result. Keep firing at Mother Brain's head once the battle resumes and it'll be over in a snap!