The next upgrade is purely optional, skip ahead to the Expansions section or all the way to the next page if you want.
Get to the Ruined Shrine where you originally got the Morph Ball and more recently picked up a Missile Expansion. Be sure to have a good supply of Missiles; around forty as a bare minimum. Jump up to the wall, then do a half-pipe jump as before, but this time get to the left ledge. Follow the tunnel until you see a Spider Ball track on the ceiling. Now follow the Spider Ball track on the ceiling as far as you can and drop down to a ledge with a purple door; this can't be reached any other way.
Tower of Light Access
Just an empty passage.
Tower of Light
The floor of this room is a pool of water and there is more going on under the surface which you can't reach yet. If you do happen to fall into the pool then climb up one of the side ramps that lead toward the entrance.
Hop up to a ledge on the far side of the room, then more ledges leading left, and finally to a platform in the center of the room. Locate the four cracked stone blocks supporting the upper part of the tower, then start shooting Missiles at them. You need to fire three at each stone; each time it flashes red to show you're having an effect and the last time part of the stone falls away.
When all four stones are done the whole layer collapses at once, lowering a ledge on the side of the room just enough so that you can jump to it. Another effect is that Plated Puffers start coming out of the vents near the platform you're on, so quickly get a scan of one of them, then jump to the ledge and then to the platform above where you're relatively safe from the Puffers. The Plated variety are just like the regular ones except you need to fire missile to destroy them. It's better to just stay out of their way here because there's no limit to how many come out of the vents and you need to save your missiles.
There are four more stones at the next level so repeat the process. In this case there are Oculi patrolling some of the stones and they can throw off your missiles if you hit one. This is a good place to get an Oculus scan if you missed it earlier. When this level collapses get up to the next platform and repeat the process a third time. Jump up two more platforms to reach your goal, the Wavebuster.
The Wavebuster is an extremely powerful weapon. Use it just like the Super Missile except it has a continuous fire feature, meaning that it will keep going until you release the trigger or you run out of ammo. It automatically targets any enemy nearby so there's no need to aim with it. The drawback, which really prevents it from being used much, is that it's a real ammo hog, using 10 missiles just to fire and 5 missiles per second until you stop.
Get back to the Ruined Fountain. The water isn't toxic any more so you can just jump in the fountain for a quick shower. If you switch to Morph Ball mode in the fountain then the force of the water will shoot you up to the ceiling where a Spider Ball track is conveniently located. Follow the track across the ceiling, then down a wall into a recess containing a Missile Expansion. Use the Spider Ball Track to get out again but there's no need to follow it all the way back to the fountain.
Get back to the Dynamo, which you will recall was reached via the Watery Hall. Jump up to the platform in the middle and use the Spider Ball track to climb into the shaft above. There is a Plazmite buzzing around here so be careful not it run into it. Get the Missile Expansion at the top and then just drop down.
The next upgrade in near so you might want to save near the Gathering Hall.