Metroid Prime/Charge Beam

Backtrack
Now that you can get little, you can pass through the wall blocking the way out of the ruined shrine. To get the Charge Beam, first go back to the Main Plaza via the Ruined Shrine Access.

Main Plaza
From here, it's on toward the charge beam. First head to the Ruined fountain via the Ruined Fountain Access. (You'll have to duck, hence the need for the Morph Ball.

Ruined Fountain
Scan: Chozo Lore: Hatchling

Work your way around the edges of the room, pausing by the fountain to scan the Chozo Lore. The first door quickly leads to some place very hot, so let's not bother going there, just now. Instead head for the Arboretum Access.

Arboretum Access
Scan: Shriekbat

Nothing important here, other than your first encounter with Shriekbats. Proceed to the Arboretum

Arboretum
Scan: Reaper Vine

Scoot past 2 Reaper vines (new!), and proceed up around the tree and through the lower door (2 more Reaper Vines) toward the Gathering Hall via the Gathering Hall Access.

Gathering Hall
Take a right to Save Station 2, then return. Proceed directly ahead to the Watery Hall Access (Avoid the Blastcaps).

Watery Hall Access
Kill the Shriekbats. Pause at the bottom of the slope to blast through the brinstone wall on the left, revealing a Missile Expansion. Proceed to the Watery Hall.

Watery Hall
Scan: Chozo Lore: Meteor Strike

To get to the Charge Beam you have to unlock a large metal gate at the top by activating 4 runic symbols. You find the first three by following the islands to your left. The fourth island has one, as does the last. Go back to the door you entered from, and as you come to island #2, you should see the 3rd symbol on the wall. Now go up the steps and follow around (mind the Reapers!) until you come to the gate. Next to the gate is the fourth symbol. Scan the fifth symbol on the gate, and it will open.

Have a Charge Beam. As an additional benefit, have some Chozo Lore to scan.

Go Home
To top things off, head back to Save Station 2 and save. (Path: Watery Hall Access, Watery Hall, Save Station 2).