It's time to face the final boss for Sanctuary Fortress. As you might expect, it will be the toughest in the game so far
Hive Dynamo Works
Get to the Hive Dynamo Works; you may remember passing through here on the way to the Spider Guardian on your first entry into Sanctuary Fortress, but there's no reason for you to have come back since. There is a White door which we will finally explore.
Hive Dynamo Access
Defeat the Ing here and switch to the Echo Visor since there is a sonic lock here. Disable the emitters as usual to open the gate and continue to the next area.
Hive Gyro Chamber
There are three exits here in addition to the White door you entered through. But there's not too much need to guess where they lead since the map of the Light side tells will give you a good idea. The Blue door in the room above the White one leads to the Sanctuary Temple on the Light side, so it's a safe bet that it will lead to the boss on the Dark side and so we'll save it for last. The Red door opposite the White one is obviously going to be a Save Station so let's save that for next to last. The only two things left are the key, which the hint system may be pointing to by now, and the door above the Red one. We'll start with the key.
Look through the window to see a large sphere with platforms circling it. It's really a giant Spider Ball Track, so hop to one of the platforms nest to the sphere, switch to Morph Ball, and grab on. The sphere is guarded by Darkling Tentacles though, so either avoid them or drop bombs to make them retract. If you fall, which is likely if you get hit by a tentacle, just climb up the Spider track under the sphere to start over; there's even a small safe zone down there just in case. Climb the small track at the top, then Boost jump to the ring around it, and Boost jump again to collect the final key.
Now start hopping platforms to reach the room above the Red door; if you get disoriented it's the one without the two columns of light.
Hive Gyro Access
There are more Ing here but otherwise just continue to the next area.
Hive Ammo Station
Refill your ammo here for the upcoming boss and go back.
Hive Gyro Chamber (cont.)
Drop to one of the lower platforms and hop into the room with the Red door.
Hive Save Station 2
It's a good idea to save because, in case we didn't mention it, there's a boss. Go back.
Hive Gyro Chamber (cont.)
This time jump to the room with the two columns of light and continue to the next area.
Hive Temple Access
Step forward to automatically place the keys in place. There is a light beacon in case you want to do some last minute healing.
Step into the lift and forward for a cut scene where a giant mechanoid is possessed by an Ing, perhaps several, and comes to life. You may recognize it somewhat since the pieces of something similar where scattered around Sanctuary Temple. But here the machine is fully assembled and functioning perfectly.
The monster leaves the Annihilator Beam behind. (It's very likely that it was using it against you a minute ago.) Pick it up and the robot disintegrates; in its place a platform rises out of the floor. Spider up the sides of the platform to where you'll be in Screw Attack range of the exits. Start by heading south, to the door with the large circular decoration above it. The Annihilator Beam opens Grey doors so use it to open the one in front of you. Remember there still aren't any safe zones here so some alacrity is in order if you're low on health.
The Annihilator Beam as a weapon has somewhat specialized uses rather than being the over powered cannon you might expect. It mixes Dark and Light energy but dilutes both in the process, so it won't be as effective as the Light Beam against Ing and you can't use it to freeze enemies like the Dark Beam. It does seek targets however, and you get both Light and Dark ammo as drops when you use it. It won't open Light or Dark doors, but it will open both Light and Dark portals.
Hive Controller Access
Use the Bomb Slot to turn the gate.
Hive Energy Controller
Get the stolen energy as in the previous versions of this room, then head back
Hive Temple (cont.)
Continue to the opposite door where you originally came in. There is another door here, but we'll come back for it after getting the Light Suit.
Hive Temple Access (cont.)
Getting across this room is a bit tricky; stand on the little balcony next to the temple, the Screw Attack up to the ledge to reach the Hive Gyro Chamber. As you go through the next two rooms, use the Annihilator Beam to activate a beacon and crystal respectively to get scans of their Super versions. These are similar to a Light Beacon and Light Crystal except they attract Dark enemies as well as destroy them.
Sanctuary Energy Controller
Continue to the Hive Dynamo Works, use the portal, then follow the route in reverse order to Sanctuary Energy Controller. Restore the energy as in the other two region. You need to go check in with U-Mos again, so we'll head back to Temple Grounds, but there are a couple of expansions to get on the way.
Expansions (Sanctuary Fortress)
There is a Grey door here which was not usable before, but now it is. You have to use the Screw Attack to reach it.
Defeat the Mekenobites here; recall that you have to use the Seeker Missile to shoot both their legs at once. About half way down the corridor you'll find a Sonic gate, but this one is special in that you need an Annihilator Beam to learn the combination before you can open it. Switch to Echo Visor and use the Annihilator Beam to shoot the speaker icon in the middle of the gate. It will play a four note melody and the idea is to reproduce that melody by shooting the three panels in front of the gate, each of which plays a note. For those who are musically impaired, shoot the panels in the order Right, Right, Left, Right. When you play the correct combination, the gate opens revealing a Missile Expansion. You now have a shortcut from Sanctuary Temple to Watch Station as well.
Main Gyro Chamber
Return to the Main Gyro Chamber and use the lift next to the Black door to get to the lower level. (You can just drop down there from the gyro room, as you may have already, but it seems more elegant to ride the lift.) Scan the hologram here if you haven't already. There is another Sonic gate here as well, so open it like the other one. In this case the combination is Outside hallway, Near lift, Hallway entrance, Hallway entrance. The gate opens, so use the Orb Cannon that's now available. You smash the dynamo core in the middle of the room and out of it pops a Power Bomb Expansion.
The next step is to go back to see U-Mos.