The mighty behemoth is back! Phantoon has experienced a growth spurt since its days haunting the Wrecked Ship on planet Zebes, and boy does it show. The massive spectre completely fills the Control Bridge's viewport - and that glass likely won't hold it back. Sure enough, Phantoon begins its onslaught by promptly smashing the glass viewport apart with its tentacles and exposing the room to the cold vacuum of space.
Samus' Gravity Suit automatically kicks in, so there's no worry of rapid decompression sucking her out into the void. Three vortices will appear throughout the chamber - each one spawns a Rage Hand. These small Phantoon cronies have no trouble trying to pummel Samus into submission, and can easily distract you from the big bad outside the window. Either quickly open up on them with regular or charged shots, or move in close and strike them with the Screw Attack to finish them in one hit. Be wary that they tend to try and avoid any close proximity hits, and keep your Sensemove handy whenever they dive at Samus.
Phantoon will begin strafing around the outside of the viewport and deploy its old blue flame trick. Scores of small blue "eyeballs" will stream into the room towards Samus - this time it doesn't look like you can destroy them (and they certainly won't be dropping any health refills) so go crazy with your Sensemove. Hold your weapon's charge and only release a shot at Phantoon's eye when there's a gap between waves of blue eyeballs. Stay at the rear of the chamber whenever Sensemoving the blue eyeballs - you might find it easier to dodge them from there.
After a few bouts of blue eyeball swarms, Phantoon will generate a vortex directly in front of its eye before the eye extends out of the body into the room. Watch out if a thin red beam emanates from the eye and pierces the ground - a huge vortex will appear on the ground and won't be good to Samus if she's standing too close. By now you'll be dancing around with the Sensemove, so you should leap clear before the vertical energy burst spews from the vortex.
With Phantoon's eye closely examining the chamber, you should have an easy target for Plasma Beam shots. Keep firing and avoiding the deluge of blue eyeballs, but pay close attention to Phantoon's massive tentacles. Eventually one of them will whip right across the room, taking out a chunk of the viewport's bracing frames. Jumping over this attack won't help much as the ever-present blue eyeballs can harm Samus even if she touches them with the Screw Attack, so try to time your Sensemove just as the tentacle whips by. Watch out for any follow-up swipes from the other tentacle.
There's rarely any time for pause during this battle, so try to preserve health and don't bother attempting to use Concentration. If you feel daring, enter first-person view and try to lock onto Phantoon's eye to summon its health bar - just be ready to Sensemove those pesky blue eyeballs. You can also try to sneak in a quick Super Missile hit. Charge your beam with 1, then hold it down while entering first-person view. Lock onto the eye and release 1 to discharge it quickly.
With Phantoon's health below 50%, it'll begin to test your Sensemove skills to the edge. The Rage Hands will return, the barrage of blue eyeballs won't stop, and Phantoon will continue to generate vortices on the ground and swat its tentacles across the chamber. Get ready to experience absolute chaos.
Don't use the Screw Attack on the Rage Hands as the blue eyeballs can still harm Samus in that state. Instead, stay at the rear of the chamber and try your best to Sensemove everything Phantoon throws at you. Clear out the Rage Hands with charged shots if you can, and watch out for the vortices Phantoon generates on the ground. This is easily the hardest part of the battle, but don't be discouraged if one of Phantoon's attacks slows Samus down. Try to end the battle quickly as you certainly won't have any chance to restore your health with Concentration here.
At last with only a tiny chunk of health left, Phantoon's eye might fall in a heap on the Control Bridge's deck. The rest is up to you - either move in and finish it with a spectacular Lethal Strike, or pound the eye with everything you've got to give Phantoon a more grisly end.