Dark Agon Wastes
The last upgrade is the combo for the Annihilator Beam. It's actually not hard to get and we'll get the remaining expansions as well.
Get to the Phazon Site as you did earlier in the game. This is the Dark version of the Bioenergy Production room in Agon Wastes. You can use the Portal in the Agon Wastes Command Center and head North. If you'd like, you can ever pick up one of the Sky Temple Keys in Dark Oasis on the way (but you'll need a Power Bomb). It is a long trek but it's all been covered before.
Once at the Phazon Site, there is a Grey door here on a ledge that's out of reach except for the Screw Attack, but you have that and the Annihilator Beam now so go through.
Ing Cache 2
The Sonic Boom is just sitting there so pick it up. It's not actually that powerful against individual enemies, but useful against a large number of enemies because it does damage over a large area. It's expensive to use though since it takes 5 Missiles and 30 each of Light and Dark ammo.
Expansions (Dark Agon Wastes)
By now you should have visited all of Agon, both Light and Dark, at least once, but there are still a few more things to do here.
Get to the Feeding Pit; it should only be two rooms away from the Phazon Site. You might have heard the hum of an expansion when you passed through this room the first time, but it was out of site. Actually it's under water and the only way of getting it is with the Light Suit. Jump in and explore until you find a small tunnel on the side near the Black door, and the Power Bomb Expansion is inside.
Expansions (Dark Torvus Bog)
Dark Forgotten Bridge
Get to the Forgotten Bridge in Torvus and use the portal there to get to Dark Forgotten Bridge. Blast open the Yellow door there, it's the one directly across from the portal in case you've already cleared the door.
There's not much to see here but a Dark Phlogus in a puddle of water. Scan the walls next to it to find a weak spot made from Denzium and blast it open, you can now grab the eighth and last Power Bomb Expansion. This gives you a total of 10 up from the 2 you got with the Power Bomb. Note that you could have gotten this expansion any time after getting the Power Bomb, but the poison water, not to mention the Phlogus, make it difficult to get without taking a lot of damage unless you have the Light Suit.
Expansions (Torvus Bog)
Get back to the Light side, get to the underwater section and go to the Gathering Hall. (It's just as easy to do this from the Catacombs.) Go through the Grey Door there.
Transit Tunnel South
Follow the tunnel to the main section where there is an underwater Morph Ball maze. Whether you enter the main section from the left or right doesn't matter because the two entrances are connected my a tunnel along the floor. Locate a Bomb Slot near the left side and activate it, this changes the flow of water just above. Get to the stream that is now going up, and double jump up, as in Transit Tunnel East when getting the Energy tank there, and to the right. Continue right to another up stream, then jump up, go left through a cage which protects you from a down stream, and jump again to another Bomb Slot. Activating it changes the down stream yuo just went through to an up stream, so backtrack to the bottom of it and double jump to the top and to the right. Continue right, boost over a gap, the go up and left to a third Bomb Slot. By now you should be able to see the expansion your after, but chances are you'll fall into the gap and will have to circle around again to get it.
By now you should have explored all of Torvus as well as Agon.
Expansions (Sanctuary Temple)
For the last expansion, work your way back to the Sanctuary Fortress. Fortunately, remember there's a handy transport from Torvus straight to the Fortress right nearby, via the Training Chamber.
Sanctuary Map Station
Return to the Map Station in Sanctuary Fortress; you may recall it's right next to the Reactor Core. Step into the Yellow light there to be transported to another room as when getting the Energy Tank in Fortress Transport Access. The 49th and last Missile expansion is there. Your total Missile capacity should now be 255, that's 245 from expansions, 5 from the Seeker Missile, and 5 from the Missile Launcher itself. It's also the last item you can get so you should see 100% items in the Pause screen.
There is still some exploration left to do both here and in the Temple grounds, but we'll cover that while we're collecting keys.