Boss Fight: Dark Samus

All things considered, your fight with Dark Samus in the Main Reactor isn't going to be too monstrously difficult. The main sticking point here is that your missiles will generally be worthless, as your alter ego will erect a Phazon shield just before they impact her, causing them to deflect harmlessly away. She also moves quickly enough to avoid your charge beam, except at close range, meaning that you'll probably do most of the damage here with your good old power beam. Just tap away at the A button while she moves around, and you'll wear her down eventually.

Try to keep the central reactor in between yourself and Dark Samus to prevent her attacks from hittin you.

Dark Samus' first form is pretty easy to deal with; she'll dash around the small little area in which you spar, firing missiles or fusillades of energy beams at you, but there's plenty of objects to hide behind, so you should be able to avoid most of the damage without a problem. After you whittle away around half of her health, though, she'll fly into the air and get a good boost of power, Dragonball Z-style. After this occurs, she'll supercharge her attacks. One of the new attacks is a comet-style charge where she'll jump into the air and attempt to ram you, while the other is some kind of super-beam weapon, also initiated from the air. Both of these are mildly damaging, but they have incredibly long warmup times, allowing you to hide behind the central pillar and avoid all damage.

The central pillar is going to be the only real hiding spot here, too, as Dark Samus will be able to destroy the four exterior pillars with either of these attacks and hit you if you're hiding behind them. You'll be completely immune to damage if you hide behind the reactor, though, so stick close to it and wait for one of your foe's attacks to end before unloading on her. She'll still be immune to most of your missile fire here, and will sometimes be just plain unhittable. She's weakest just after landing from the comet charge; you'll notice a blue shroud around her as she's standing up from this, but if you wait until she stands up, she'll be vulnerable for a split-second, letting you land a full chargebeam shot on her. Lather, rinse, repeat until dead, then head upstairs to grab the Dark Beam.

Light Beam

Now that you have the Dark Beam, you'll be able to move through black-sealed doors, and the security doors with the small crystals in them. Head back through Security Station B, and check your map for the small room off of the Biostorage Station. You can fight your way back there to get another Missile Expansion, but beware; the Metroids in the room adjacent to it will break out of their cages and attack you if you do so. There are only two of them, though, and their charge attack can be easily dashed around, so missile them to death and grab the expansion.

When you're ready to get back to Dark Aether, return to the Command Center and shoot the inactive portal with your Dark Beam. (Note that portals appear on your map with a large P symbol.)

The room you find yourself in, the Dark Entry, holds the second Dark Temple Key. In order to reach it, though, you'll need to lower one of the platforms, which you can do by scanning their bases until you notice an object made of Brinstone inset into one of them. Destroy this with a missile, then shoot the crystal within with your Dark Beam to cause the platform to recess into the floor, giving you a jumping path to the Dark Temple Key. The door nearby can be opened, but it doesn't lead anywhere, so jump back across the platforms and head through the other dark door.

There's only path to follow here, which will lead you to the Hall of Stairs. The central pillar here has another crystal on its upper end, so locate it and hit it with your Dark Beam to lower it a bit, allowing you to pass up to a save station.

In the Phazon Site, you'll have to pass through a security gate, which can only be unlocked if you scan three security terminals scattered around the room. The only one that's mildly difficult to find is hidden behind a stack of crates on the lower level here, but the other two are easily spotted, so scan them all; you can actually scan each of them twice, including once after you use them to break down the lock. You'll eventually wind up in the Feeding Pit, where you'll need to locate some more crystals on pillars to knock them down before jumping up, but be careful of the muck at the bottom of the room, which will prevent you from space jumping. In the Ing Cache 1, you'll finally be able to nab your Light Beam.