After you activate auxiliary power, you have to restore the ship to full power.
Fix the Reactor Core
After the tough battle with Yakuza, you'll want to save, so use the bottom right door to reach the Save Room that is now operational. You are going to need your energy maxed out for the next part, so if your tanks are not full, exit the Save Room, kill the three Keyhunters on the ground to the left, collecting their free-floating X, return to the Save Room, and repeat until your energy tanks are full.
Once you are ready, head to the middle of the Reactor Core room and Space Jump up and left. There is a ledge you can only reach by Space Jumping up above, below the top left door. Get up there, avoiding the flying Keyhunters around, and Space Jump up above to where there are vines blocking a narrow tunnel. While Space Jumping, shoot the vines to clear the way to the tunnel. Once you can get up there, go through the tunnel.
Use a Power Bomb to quickly destroy the vines blocking this narrow tunnel. Exit left.
You will hear the ominous footsteps of the SA-X. Head to the left, wait a little bit, then when you're ready for the toughest chase in the game, stand up and get on the Pit Block to the left to fall below and face your enemy.
Shoot the SA-X immediately with an Ice Missile, then jump over it and exit the room (shooting it with another Missile if you think you need to buy yourself more time). In the next room, turn and face the door and start shooting a ton of Ice Missiles to freeze the approaching SA-X once more. When it is safely frozen, quickly get into a ball where you're standing and drop a Power Bomb to break open the wall to the left, then QUICKLY stand up and start hammering the SA-X with Ice Missiles again before it can thaw out. When you're ready, jump over the obstacle to the left and start running left to exit this room. The SA-X is still coming. 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 necessary (and if you are able to... you probably won't be). Once you get through the next door, quickly jump and pull up onto the wall, and stay there. The SA-X will come in, pause for a second, then leave. It's gone; you're safe again.
Your energy may be really low after your encounter with the SA-X, so take extreme caution as you proceed.
Exit to the right (don't worry; the SA-X is not there) and jump and shoot a Missile down at the floor to the right of the brown vegetation to the right of the door. If you aimed right, you'll destroy a Missile Block. Jump and shoot your regular beam to destroy the rest of the floor below. Once you've fallen down to the next area, head through the door to the left.
Space jump up through the shaft until you see some vines where some Keyhunters are trapped. Don't shoot the vines; you don't want to deal with any Keyhunters you don't have to if you're low on energy. There is one Keyhunter out in the open above, but it shouldn't come down to you. Shoot the empty vines to the left, then shoot below you to destroy the rest of the vines and break through the floor. You reach a door leading to the left. Exit through it, then exit left again.
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 little Puyo (regaining some energy from their free-floating X), then continue right for a Power Bomb Tank. Space Jump back up to the ledge above, and head right to a much-needed Save Room. You can keep going into the Save Room and back out, killing the Puyo to regain the energy you lost running from the SA-X, though you will have to use a lot of Power Bombs to get back through the wall below.
When you're ready, go back to the Save Room and exit right twice. Shoot the blocks above to break open the ceiling. Space Jump up to the next area. Shoot through the vines to the right, trying not to free the Keyhunters, and shoot up to open a hole above. Jump up through it onto a ledge to the left, then up to the next ledge and you'll be faced with a Living Door. Carefully destroy it, collecting the much-needed red X it releases, and go through the door. You'll fall through some Pit Blocks to a boss below.
This plant-like monster is the source of the roots surrounding the Reactor Core. Two flowers to either side of you will shoot out spores that will hurt you if they touch you. You'll have to keep shooting the spores to keep them from hurting you. There are three man-eating plants (woman-eating plants?) below that will chomp you and hold you for a few seconds if you fall into one, so be careful. DO NOT try Space Jumping out of the plants; you will stay stuck and continue to be eaten. Jump straight up to get out. Clearing away the spores, you'll want to get up on the platform close to Nettori and stay there, shooting Ice Missiles or charged shots at the thing. You will have to keep facing left and jumping a little bit to shoot the oncoming spores from the left flower so they won't hit you and knock you into one of the carnivorous plants. If you want to clear out all the spores and damage Nettori a little bit, drop a Power Bomb.
After doing a lot of 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. Shoot Nettori with Ice Missiles (which are more powerful but will be deflected by the Plasma Beams) or charged shots (weaker but will get through the beams) until it becomes a Plasma Core-X.
Run to the newly-opened area to the right and fight the Core-X, which has an eye and will shoot Plasma Beams when you shoot it. Kill it as you have killed other Beam Core-Xs, and collect the Core-X to regain your Plasma Beam ability.
Sector 2 (TRO)
With Nettori destroyed, the Reactor Core has gone back online and hatches and elevators are once again active. Exit through the hatch to the right.
In this room with trapped Keyhunters, head down to the door below and go through. Continue left (shooting Plasma Beams to kill the Keyhunters in the way) and through the door to the left. Go left one more time to a Save Room, then exit left yet again. Head left, fall below, and exit through the door here. Get onto the platform below briefly and shoot up to kill the Keyhunter above. Then Space Jump up the shaft (trying to avoid a Keyhunter above) to a small tunnel with a door you can now reach, now that the Keyhunter cocoon is empty. Go through.
Drop a Power Bomb to reveal the Pit Blocks here. To get to the Power Bomb Tank, get onto the rungs above and shoot down below at the right-hand Ripper with an Ice Missile to freeze it. Then, standing on the frozen Ripper, hold L and down and face left to freeze the second Ripper when it's beyond the barrier in the way. Carefully ball jump onto the second one, then stand up and jump to the Power Bomb Tank. You can also freeze the Ripper below the top two from the ladder to the right, in case you keep falling through the Pit Blocks.
Once you've collected the Power Bomb Tank and fallen through the Pit Block below it, bomb where you land to find another Power Bomb Tank. You'll fall further below, to the bottom of the room. Lay another bomb to get out of here. Climb your way up the ladder avoiding the Rippers and exit this room.
Drop down below to where you came from, and go back through the door you originally came in through to the big room. Space Jump back up to the ledge above leading to the Save Room, and go through and save. Exit right.
Shoot the Keyhunter above and Space Jump up the shaft, trying to avoid Reo above that will float down at you. Don't go all the way to the top of the shaft; get onto the first ledge to the right. There is a hidden tunnel in the right wall, so roll through it and you reach a Recharge Room. Recover your weapons and energy, then roll back to the shaft and Space Jump to the top. Go through the door to the right.
Get rid of the Owtches and get up against the right wall. Jump and hold right against the wall to grab a hidden ledge. Pull up and roll right, head to the right and turn around to face the wall jutting down. Jump and shoot it to reveal a hidden Energy Tank. Collect it and roll back through the tunnel, returning to the shaft. Exit through the top left door.
Kill the Keyhunters and then roll through the tunnel to the left. Use a Power Bomb to destroy the block in the way, then head for the Navigation Room. Uplink for your briefing. Adam is surprised you recovered your Plasma Beam ability, but advises you to continue to avoid the SA-X, as you still have a few more abilities to recover. Adam will sense trouble, and will isolate the cause as an explosion in the ARC Data Room that has caused staggering damage. Head for Sector 5.