After you activate auxiliary power, you have to find the source of the vegetation that is preventing the Reactor Core from working.
Fix the Reactor Core
In the Reactor Core room, go through the bottom right door if you want to save the game. If you need to replenish your health, leave the room and kill the nearby Keyhunters, then go back to the Save Room and repeat until your energy tanks are full.
After that, find a narrow tunnel in the left wall, below the upper left door. Shoot the vines that are blocking the tunnel, then roll through it. In the next room, use a Power Bomb to quickly destroy the vines blocking this narrow tunnel. Exit left.
You will hear the SA-X's footsteps in this room. Go to the left. When you land on the small block to the left, you will fall through a Pit Block and be face-to-face with the SA-X. Shoot it with an Ice Missile, then jump over it, shoot it with another Ice Missile, and exit the room. In the next room, turn and face the door and start shooting Ice Missiles to freeze the approaching SA-X once more. When it is safely frozen, quickly roll into a ball where you are standing and drop a Power Bomb to break open the wall to the left, then quickly stand up and shoot more Ice Missiles at the SA-X before it can thaw out. When you are ready, jump over the obstacle to the left and start running left to exit this room. The SA-X is still following you. Hold L or left-up to shoot diagonally upward so you can hit the lights and open the gates more easily. Do your best to jump through the gates, turning around to freeze the SA-X if you think that you can do it quickly enough. After you go through the next door, quickly jump and pull yourself up onto the wall, and stay there. The SA-X will come in, pause for a second, then leave. You are safe for now.
Exit to the right (the SA-X will not be there) shoot a Missile at the floor to the right of the brown vegetation. If you want to be sure of the correct spot to shoot the missile, use normal bombs on the floor to find it. Then shoot your normal beam into the hole that you opened, and go down through the hole, shooting more beams at the floor if necessary, to reach the lower area. Then go to the left and go through the door there.
Space jump upward through the tall room. Remember to wait until you are falling at maximum speed before starting the next Space Jump, and try making each jump short so you can go upward more quickly. Go upward until you see some vines where some Keyhunters are trapped. Don't shoot the vines. There is one Keyhunter out in the open above, so avoid it if it flies toward you. Shoot through the vines in the lower left of the upper area, then shoot the floor to destroy any remaining vines and break through the floor. Go through the door on the left, then in the next room, go through the door on the left.
Jump over the wall here, then Space Jump up to the top left of the room, onto a ledge. From where you land on the ledge, drop a Power Bomb to open the wall below you. Space Jump down to it. Shoot the wall to the right and carefully destroy the Puyos, then go to the right to get a Power Bomb Tank. Space Jump back up to the ledge in the upper left of the room, then go to the right to find a Save Room.
In the Save Room, go through the door on the right, and in the next room, go through the door on the right. Shoot the ceiling to open a hole, then Space Jump up to the next area. Shoot through the vines to the right, but try not to free the Keyhunters, and when you reach the right side, shoot upward at the upper right corner to open a path upward. Go up and land on the ledge to the left, then go up to the next ledge and kill the Living Door and take the red X that it drops. Go through the door. You will fall through some Pit Blocks to an area with a boss battle.
This plant-like monster is the source of the roots surrounding the Reactor Core. Two flower-like plants near the ceiling will continually spit spores that will hurt you if they touch you. Keep shooting those spores throughout the battle.
In the floor, there are three carnivorous plants. If you fall into one, it will bite you and hold you for a few seconds. If this happens, be sure to jump straight upward to get out. If you try Space Jumping instead, you will stay stuck in the plant and continue to be eaten.
After shooting the spores, go onto the platform near Nettori. Stay there, shooting Ice Missiles or charged shots at the monster. Shoot the spores to prevent them from knocking you into one of the plants. You can drop a Power Bomb to get rid of the spores and do a small amount of damage to Nettori, but the spores will keep coming out.
After you have done enough damage to Nettori, it will start shooting Plasma Beams at you, and the flowers will stop shooting spores. Jump to avoid the low beams, and crouch to avoid the high ones. Ice Missiles will bounce off of the Plasma Beams, but charged shots will not be deflected. Keep shooting Nettori until it transforms into Plasma Core-X.
Go to the right to continue the battle. The Plasma Core-X has an eye and will shoot Plasma Beams when you shoot it. Jump to avoid the beams, and remember that the Core-X will shoot a beam if you don't attack it for a while. After you defeat it, collect the Core-X to regain your Plasma Beam ability.
Sector 2 (TRO)
Now that Nettori has been destroyed, the Reactor Core is back online. Hatches and elevators are once again active. Exit through the hatch to the right.
In this room with the trapped Keyhunters, go down to the bottom of the room and go through the door on the left. Shoot Plasma Beams as you go to the left through this room to kill the Keyhunters in the way, then in the next room, go through the door on the left to reach a Save Room. From there, go through the door on the left.
In this large room, go to the left and fall down to the bottom. Go through the door on the left. In this room, go to the left to land on the platform just below the door, and aim upward to kill the Keyhunter before it can hit you. Then go up the tall room, avoiding the Keyhunter above, and go to the door on the left that has an empty cocoon in front of it. Roll through the tunnel to reach that door, and go through it.
Drop a Power Bomb to reveal Pit Blocks here. To get to the Power Bomb Tank, grab the rungs in the ceiling and shoot an Ice Missile at the right-hand Ripper. Stand on the frozen Ripper, keep freezing it if it starts to thaw, then aim diagonally down (hold L) and shoot an Ice Missile at the other Ripper when it is beyond the barrier to the left. Carefully ball jump onto it from the first Ripper, then stand up and jump to the Power Bomb tank.
After you get the Power Bomb Tank and fall through the Pit Block below it, drop a bomb when you land. You will get another Power Bomb Tank, then you will fall to the bottom of the room. Drop another bomb and roll out of this area, then go up the ladder and go through the door at the top.
Roll through the gap in the wall, then go downward and go through the first door on the right. In this large room, go to the right and Space Jump over the wall on the right, then go through the door. Keep going to the right until the map shows that you are above the Save Room. Space Jump up the tall room, but be careful of the Keyhunters and Reos that will fly toward you. When you reach the area that has a rectangular platform floating in the middle, go to the right wall and roll into a ball. Roll to the right through a hidden hole in the right wall. You will reach a hidden Recharge Room. After you recharge, leave this room and Space Jump to the top of the tall room. Go through the door on the right.
Kill the Owtches in this room, then go to the right wall and jump up against it to grab a hidden ledge in the right wall. Pull yourself up and roll to the right, then in the next area, stand next to the wall on the right, then face the left wall and jump up and shoot the hanging wall, one square below the top. You will find a hidden Energy Tank. Take it, then make your way back to the tall room. Go through the top left door.
Kill the Keyhunters, then roll through the tunnel on the left. Use a Power Bomb to destroy the block in the way, then go to the Navigation Room. Adam will tell you to investigate massive damage in Sector 5. Take the elevator there.