Time to confront the final bosses in the game. The battles will be long and difficult so get ready for a challenge.
Sky Temple Energy Controller
You see the enegry you're after, but a creature comes through the ceiling and snatches it away.
There a ledges on the walls that allow you to get to the upper ledge. Locate the Save Station here and use it. There are also some Ing storage pods in case you need last minute refills. There is also a transporter hologram in the middle of the room in case you want to bo back. Use the door opposite the Safe Station.
Wall Jump up the shaft and go through the door at the top.
You see the Energy Core sitting in the middle of the room, but when you approach a creature looking like Cthulu pounces and a battle begins.
This is the first of three phases in this fight, but this part is actually not as bad as you might expect. Start by getting scans of both the head and body. You need to shoot the ends of the monsters tentacles to get them to retract, but they move around a lot so you'll have a hard time with accuracy. The charged Light Beam is useful here because its shot gun effect will help get in a hit, but the regular Light Beam is almost as effective and uses less ammo.
Meanwhile, the monster attacks you with its tentacles in a number of ways. It will take swipes at you to for one thing, but you can sometimes avoid this by staying out of reach, but don't back into the Phazon at the edges. It may also start swinging it's tentacles in a wide circle, but you can jump over them like a skipping ropes. It can also create bombs with a wide area of effect, if you listen for these you can often Boost out of range before they hit. Another attack is to create warp windows through which more tentacles appear, so you'll want to watch out for these and keep your distance.
When the last tentacle has retracted the creature reveals its eye. Be sure to get a scan here because it's easy to miss. The eye has two shields and the only way to hit the eye itself is to fire into the gap; if you remember the Parasite Queen battle at the start of the previous game then this will be familiar. The eye will shoot laser beams back at you so keep moving when you see it charging up. Shooting the eye is the only way to actually damage the monster so try to make every shot count. Eventually it recovers and you're back to to fighting the tentacles again. As the creatures health gets low it steps things up by sprouting more tentacles and using more powerful attacks.
Chrysalis Emperor Ing
When you've defeated the first incarnation of the monster, it forms a chrysalis to protect itself while it tries to recover. This is actually the easiest of the three phases. The room fills with toxic gas, scan the Chrysalis quickly then use Spider Ball to latch on and roll up out of the gas. There are weak spots on the shell that will occasionally spawn Inglets. When you're close to a weak spot, it will bubble with Dark energy for a moment then a tentacle will spawn for a short time. Drop bombs, and attempt to time them so that they explode on the tentacles to damage the Chrysalis. If you get knocked off, spider back up swiftly out of the gas. You'll be better off attacking the lower spots first because the gas gradually rises. Hopefully you came with a stash of Power Bombs. This fight will go quickly if you can lure out several tentacles and drop a Power Bomb. The Inglets drop significant health pickups, so you'll want to gather as many of these as possible; you may even come out ahead by the time this part is done.
Mutated Emperor Ing
If you played the first Metroid Prime, this phase will look and be fairly familiar to the first phases of the original Metroid Prime fight. Don't forget to scan. The most critical part of surviving this fight is still avoiding the Phazon at the perimeter of the room. Emperor Ing has a glowing heart that occasionally shows through its mouth-like oriface--this is its only weak spot. The color of its heart will occasionally change, cycling among orange, purple, and white. When orange, Emperor Ing cannot be damaged--one hit with a Super Missile will force it to change to purple or white. When purple, blast it with the Light Beam; when white, blast it with the Dark Beam. Occasionally Inglets and Nightbarbs will spawn and they can be killed for extra pickups. Charged blasts from the Light and Dark Beams will do decent damage, but don't waste your ammo if you're struggling to hit. Hitting with several regular shots is better than missing with charged shots. As its health depletes, the heart glows brighter until you land the killing blow.
Escape from Dark Aether
After defeating Emperor Ing, Samus collects the last of the energy, causing Dark Aether to become unstable. A countdown timer starts for 8 minutes with some music that Metroid veterans will find pleasingly familiar. It sounds like a lot of time to escape as you quickly make your way out of the Sanctum, but when you arrive back at the Sky Temple Gateway, your mysterious nemesis shows up again.
This fight may be particularly stressful as you have to beat the countdown timer, but with the right strategy there is plenty of time. Scan Dark Samus quickly as you begin so you don't forget. If you have plenty of energy, a passive attempt at dodging Dark Samus's attacks is good enough. The fight starts like many other Dark Samus fights, except this time its Phazon infusion overloads your Dark Visor. Dodge Dark Samus's attacks until it phases out; don't bother trying to harm it because all attacks will bounce off of its Phazon shield. When phased out, quickly switch to the Echo Visor and launch Super Missiles until it phases back in.
Once enough damage has been done, Dark Samus will shed the suitlike appearance and become a being of pure Phazon. Time to overload again. Scan Dark Samus's final form and you should get 100% scans if you've been following along the guide. Dark Samus will float just above the platform with a Phazon shield. It charges up and fires large shots at you. These are easily dodged by jumping to the side--keep a lock on and keep your Charge Beam up. When the Phazon shield grows and shrinks, Dark Samus will fire smaller shots at you. Touching 3 of these with your Charge Beam will turn it blue with Phazon, then you can fire it back at Dark Samus to do damage. Note that any Phazon shots that hit you after you have absorbed 3 may cause damage. Repeat until it dies.
Samus barely escapes through the portal and returns the Light to Aether. Dark Aether collapses.
Enjoy the ending sequence!