This is the second time Samus has stared into the maw of a Queen Metroid, and the creature's 3D debut is epic from the start. As the beast stomps its way into Room MW, a single Metroid will spawn from the Queen's back. The Queen will then proceed to outright charge at Samus with a gaping wide maw. Instantly use the Sensemove to leap clear (usually two are needed) - you don't want to lose health in this opening strike. Sensemove to the left to avoid collisions with the specimen tanks.
Initially there's nothing you can do to harm the Queen itself, instead you'll need to fend off the pesky Metroids it spawns. These ones are still vulnerable to cold, but won't be pushovers. They tend to dodge your shots with extreme ease and can be hard to track with their fast movements. No matter, just be ready to Sensemove when they move in for the kill. As always, if a Metroid latches onto Samus it'll begin sapping your energy, so simply enter Morph Ball mode and drop a bomb to break free. Try to avoid this as much as possible however - the Sensemove should keep you safe.
Try to use charged shots against the Metroids, and utilise the instant charge when Sensemoving. Oddly, it seems that Metroids can be frozen by single shots of your Plasma Beam, but they tend to avoid them with ease. Run over to a corner of the chamber to steer clear of the Queen - often it'll keep to the center of the room and might smash the specimen tanks to keep itself entertained.
Staying in the corner will also help to score hits on the Metroids, as the Diffusion Beam will spread out and cover a wider area. If your beam hits a wall instead of a target, splash damage might still freeze any nearby Metroids. Once a Metroid is frozen, it'll fall haplessly to the ground. You'll need to pump three Missiles into a single Metroid to finish it off. Alternatively, use a single Super Missile to conquer one instantly.
With the first Metroid taken care of, scores of the parasites will continue to spawn from the Queen's back. Be ready to Sensemove the incoming barrage, and remember to lay bombs in Morph Ball mode if a Metroid attaches to Samus. Stay in a corner and unleash a charged shot as they cluster around Samus to easily freeze more than one at a time. Just be sure to freeze all active Metroids before entering first-person view to deliver Missiles - you don't want one grabbing Samus while you're vulnerable. This may be difficult to achieve, as one of the annoying bugs always tends to remain unscathed while the rest lie frozen.
Be patient - try to quickly lock onto a frozen target and release Missiles (or Super Missiles - the splash damage may harm surrounding frozen Metroids). But always be aware of any potential active Metroids - they have a tendancy to roam about behind you, completely out of sight. Have your Sensemove ready to avoid their cheap tricks. Don't worry if a Metroid unfreezes before you can finish it off, as any damage you inflict on them will remain. You might also want to stay as far away from the Queen as possible; while it doesn't attack Samus directly, it can generate a shockwave that unfreezes any immobile Metroids.
Also, if a cluster of Metroids end up frozen, lock onto one and charge up your beam. Release a Seeker Missile to take out the first one and harm the others.
Avoiding Metroids will be tough, especially on Hard mode. If you need to use Concentration to replenish health or Missiles, wait until all active Metroids are laying frozen on the ground before using the technique. Eventually the swarm of Metroids will dry up, and with the last one defeated the Queen will try something different.
Huge purple crystalline growths will sprout from the Queen's head and neck - now we can take the fight to the big bad itself. Take extreme care at this point, as the Queen won't hesitate to try and ram Samus into a corner. Also watch out if it charges up glowing energy along its neck - this precedes an enormous flame breath attack spread out over a wide angle - one hit from the fire on Hard mode and it's all over. Using the Sensemove doesn't seem to work too well (probably thanks to the enormity of the fire's range), so leap into the air and Space Jump around to one side of the Queen.
Normally, you can use the Screw Attack to fly through the fire and Samus won't be harmed. Unfortunately, I've seen instances where the fire has harmed Samus, even though the Screw Attack was clearly active. I don't know if this is a random glitch in the game, but regardless, try to avoid flying through the fire. Either try to Space Jump over the flames, or stay on either side of the Queen (never directly in front of it) and run to the sides to outrun the flames entirely.
The crystalline growths are the obvious weak point: send charged Plasma Beam shots into them to slowly weaken the creature. You can also try to use Missiles, Super Missiles or the Seeker Missile (at least to scan the Queen and reveal its energy bar), but only after the Queen's flame attack subsides.
You might find that constantly flying around the Queen with the Space Jump works well to avoid both its attacks; land when you're safe and release a charged shot (and when the Queen rams a wall, see if you can spot the green slime ejecting from its exhaust pipes). Take care if you ever find yourself quite some distance away from the Queen - it'll aerobically turn 180 degrees and attempt to stomp down on Samus (if she's standing behind the Queen). Use the Sensemove to help avoid the surprise.
Eventually with enough punishment, the crystalline growths will begin to break off - the loss of each one will sap a chunk from the Queen's health. Keep orbiting the Queen with the Space Jump, and open up with the Plasma Beam (or any ballistic attack). Eventually all the growths will break off, fully draining the Queen's health.
After the following scripted sequence plays, you'll find yourself back in control of Samus in first-person view as the Queen lays on its side up ahead. Quickly lock onto the exposed underbelly of the target and let rip a few charged shots to severely drain its newly-regenerated health bar. Eventually the Queen will regain its composure and stand up. It'll open its massive maw and begin charging up a swirling vortex of energy. If you don't act fast enough, a massive lethal energy beam will end Samus' day instantly. So don't wait - strike first.
If you lock onto the Queen's open mouth, don't be surprised to see the words "Grapple Beam" appear on the target reticule. There's nothing else to it, let's relive old 8-bit memories and leap inside the Queen's mouth. After grappling inside the Queen's mouth and automatically entering Morph Ball mode, Samus will once again find herself inside the belly of the beast.
For first-timers this is one of those moments in the game that can easily stump you, as Morph Ball bombs don't seem to harm the Queen at all (very much unlike last time in Metroid II), so what can you do? The answer is momentously simple and usually far more rewarding if you can figure it out for yourself. Here's some hints to help you work out the answer:
Just have a think about what weapons Samus normally has in her fully-equipped arsenal. The game doesn't tell you, but there are no more restrictions in place anymore - you can now use anything you want from this point onwards. What other weapon would Samus normally have access to while in Morph Ball mode? If that doesn't help, try this: what is the last remaining ability yet to appear in Samus' arsenal, one that you've used only once so far, way back during the opening tutorial at the start of the game? Check Samus' upgrades if you need reminding. That should do it!
If you've given up and need the solution, click the link below for the answer:
One final note: this battle is broken up into three segments, and thankfully if you lose during the second or third stages, you'll be taken back to the start of that same stage - so you won't need to face the Queen again from the very beginning.