Didn't the Care Bears Use a Sunburst Attack?
You may have already received another hint as to the location of your next critical objective, but you should ignore it for now, as the Sunburst is not too far away. Instead of heading back into the Fortress, make your way back to the elevator leading to the Temple Grounds; you'll find yourself back in the GFMC Compound. If you make a short trip down to the Dynamo Chamber, you can find a Power Bomb Expansion hidden inside a wall there, so grab it, then go back to the Compound. There is a yellow door here, but it leads to a dead end at the moment. Instead, head back up to the Great Temple via the elevator nearby and take the C Access back down; this will let you out near the Path of Eyes, from which you can access the Windchamber Gateway and, hence, the Grand Windchamber.
The puzzle here isn't too difficult to figure out. You can't do much on the Aether side of it, though, so warp over to Dark Aether with the portal, then start using the spinners. There are four spinners, each with its own kinetic cannon; you'll need to use them to line up the central cogs so that they're lined up top to bottom and also lit up. They can be rotated around between four positions, but only two of the positions will actually light up. When you have the four platforms lined up in one of the lit-up positions, you can jump to that platform and use your seeker missiles to hit all four of the purple targets simultaneously. You'll need to do this twice before you unlock all four of the platforms, at which point you can return to Aether and use the grapples to reach the sole cannon there, which will give you access to the Sunburst. Now that you've got it, you can return to the Sanctuary Fortress via the elevator near the GFMC Compound.
When you return to the Fortress, proceed back to the Hall of Combat Mastery and use the elevator nearby to reach the Main Gyro Chamber. Your goal is located beyond the yellow door here. (You'll note that there's a yellow door at the end of the Spider Guardian's lair; if you wish to go through and retrieve one of the Sky Temple keys, you can do so, but you won't need it until later in the game.) If you take the elevator near the door up to the upper observing platform, you can destroy the debris there with a power bomb to reveal another two-dimensional lock for the inner ring of the gyro. It can be difficult to spot, but this ring has a spider track attached to it, so get onto that, then boost your way through the cracked glass on the far side. Before you do so, though, be certain to save your game in the room below, as there's a boss fight coming up.
Boss Fight: Dark Samus
Dark Samus 2 is much tougher than she was earlier, but you should have plenty of health at this point in the game, and her attacks aren't too much tougher to dodge. Her main new features are a boost ball attack, which you can either try and hit her or just jump around to avoid it; an ice beam attack, which is easily escaped by quickly tapping B; and an invisibility mode, which can be neutered with your dark visor.
Your best bet for damage here will be super missiles, we find. They will sometimes miss or bounce away harmlessly due to her phazon shield, but they'll connect often enough to do serious damage to your foe. As before one of the best times to hit her is just after she lands one of her comet charges; your lock will probably dissolve as she stands up, but you should be able to just anticipate her position and fire it manually into her back just after the phazon shield drops. Another good time to use it is while she's invisible, so switch to your dark visor and go to town. Eventually she'll die - again - and, of course, trouble you no more for the rest of the game. We're serious, this time.
Afterwards, drop down onto the small platform nearby and walk along the ledge until you reach the dark portal. Head through and spiderball over to the main platform, then use the spinner to rotate the spidertracks in the middle of the area until they lock into place. Follow the tracks, boostjump to the far platform, then leap over to the portal and jet back to Aether to obtain the Echo Visor. You can use it to track down the three sonic generators that are restricting access to the elevator leading downwards; shoot them to unlock it and return to the Gyrochamber.