The hint system points to a new upgrade and the path to get there goes through the Arboretum. There is a major boss battle this time and nearest save point is the one near the Gathering Hall some distance away.
Return to the Arboretum. You need to get to the top of the room, but the door there is locked by four runic symbols as in the Watery Hall. So you might as well scan the symbols to unlock it as you make your way up.
First go to the bridge that connects the tree to the ledges on the perimeter. The first symbol is right where the bridge connects to the tree. Drop down to the ledge next to this and look across the water to a ledge under the bridge with what looks like red Tangle Weed. (You'll be able to identify this in a bit.) Shoot at the weeds to make them retract and reveal the second symbol. Go back and cross the bridge and start scaling the ledges right, but locate and destroy a wasp nest on the tree before you get too close and the wasps attack.
There is a channel in the wall, so switch to Morph Ball and follow it, clearing the stone blocks with bombs as you go. Switch back when you exit the channel and find the third symbol next to a step. Before going farther, locate a second wasp nest on the tree up ahead and take it out before it makes any trouble.
Hop up the next step to another channel in the wall. This times it's blocked by the red weeds; scan them to learn that they're called Venom Weed. They look and act much like Tangle Weed except they're toxic. Shoot them to make them retract, then switch to Morph Ball and get through the channel before they reappear.
Go up a couple more steps, then turn turn around and follow the wall to the left instead of to the right, and soon after you land on the ledge with the gate. The final symbol is on the tree across from this.
The open gate reveals a blocked tunnel, so drop a bomb to open it and go through. The fire a missile to unblock the door and go through.
This passage is guarded by Venom Weed and Reaper Vines. Lay down some fire to clear a path in the weeds before shooting a vine to make it retract, then step forward to next patch of weeds to do the same.
More Venom Weed and Reaper Vines are here. Be sure to get the boxes near the end to top off you health and/or missile supply.
When you enter the room a giant carnivorous plant appears in the middle of the room. Vines grow in front of the door preventing your escape and a battle begins.
Flaagra was the source for the toxins in the water, so you can now safely take a dip anywhere in the the Chozo Ruins. The vines that grew around the door where you came in are still there, so you can't get back that way. There is another door here though; collect the Varia Suit to unlock it. With this suit you're starting to look a lot like you did at the start of the game.
The Varia Suit doesn't unlock any new exploration in the areas you been to so far; the one additional room in the Chozo Ruins that you can enter now is still a dead end. It does allow you to withstand the heat of the next area, Magmoor Caverns, the highway of Tallon IV. The way out of this room happens to lead to an elevator which descends to Magmoor.
Sun Tower Access
Take a swim through the water and turn right at the patch of Tangle Weed when you're on land again. There are crates with health pickups with 100 HP each here, so be sure to get them, doing a scan first, to recover from the battle you were just in.
Farther down the passage you encounter a Pulse Bombu. You don't have any weapons that can harm it at the moment, so just time your way through the bombs it drops. Don't use your charge beam near it since Bombus are attracted to the energy.
You start at the top of long vertical shaft. Jump across to the dark ledge opposite, then scan one of the little bugs crawling around the wall. It's an Oculus and it's harmless if you stay out of its way.
Drop the rest of the way down, it's a long way but your suit can handle it. What you need to worry about are the four wasp nests at the bottom. You can just make a beeline (get it?) for the door or stand and fight. If you make a fight of it, shoot missiles at the hives first so more wasps don't appear, then clear the wasps that are already in the room. There is a box here with an Ultra Energy to recover after this fight. With the wasps gone you scan the inscription on the wall in peace, then continue to the door.
Transport to Magmoor Caverns North
You've been here before on the way to get the second Energy Tank. This time take the lift.
Transport to Chozo Ruins North
The lift end here. There is only one door so go through.
You start at the top of another shaft. This time there are moving ledges on the walls which you can use as lifts to get back up from the bottom. Use the lifts to ease your way down gently or just drop down quickly; you don't get hurt either way.
Start following the passage at the bottom, but watch for Shriekbats in several locations. Continue and get a scan of the Grizby near the end. This is very similar to a Zoomer except that you need to missile to destroy it.
Turn around and use a missile to clear the door at the corner.
Save Station Magmoor A
Unless you went out of your way earlier, this is the first chance to save since the boss battle so it's a good idea to do it now. There will be another save point a bit later but it's better to be safe.
Go back and continue to the end of the passage in the Burning Trail.
It's at about this point where you'd be stopped without the Varia Suit. The heat from the Lava, not to mention the jets of flame, would be too much for your Power Suit to handle and you would lose energy quickly.
Clear the Grizbies from the stepping stones and hop across avoiding the flame jets. There is a Burrower in the next tunnel. Lock on and wait for it to jump, then quickly shoot and dodge at the same time. With a bit of luck you should hit it while avoiding whatever it is that it spits at you. Get your scan first though.
The floor here is covered with lava and it will take some platforming skill to get across. But first you must deal with the large fire breathing serpent/worm the pops out of the lava. It's a Magmoor, one of the creatures that these caverns are name after. Stay out of range of its breath and start shooting; it can be defeated with any weapon, even the Power Beam if you hit it enough times. It's weak to Ice based weapons, but since you don't have any of those at the moment you'll just have to file that information away for later.
The other creatures here, which look like jet-powered soccer balls, are Puffers. It takes just one shot to destroy them, but they leave behind a cloud of toxic gas so shoot them from a distance and stay away from the cloud that remains.
Clear the section and follow the platforms around the side. Watch out for the floating, spool-shaped ones since they start to sink when you stand on them. At the other end of the path are a few crates blocking a sandstone wall. Use a bomb to remove the wall, opening up a tunnel with a similar wall at the end.
The next section is similar to the first but a but shorter. Hop the platforms again to the next door.
There is a wall blocking the way forward and the only way across, at least for now, is under the floor. This is guarded by Triclops (Triclopses?). They only go after you in Morph Ball form, and if they catch you they will unceremoniously deposit you outside their territory, costing you a bit of health in the process. You can defeat them by leaving a bomb in their path since they swallow it and it explodes inside them. There is a bit of a knack to carrying this off, so you might as well get in a bit of practice now.
Scan one first, then switch to Morph Ball and go through the hole to get under the floor. Defeat or dodge the Triclops and get to the opposite hole, then go through the door there.
Get through the steam vents and wait for your visor to defog. You're now on a ledge over a large room; there are Puffers floating around and Triclops under the floor. There are platforms leading to the left and these lead to your destination—the hint system may already be pointing you there. First there is a little side trip though.
Drop off the middle of the ledge, then turn around to find a little cave underneath. Step into the cave, switch to Morph Ball, and go into the tunnel to start exploring under the floor. Follow the right wall to get to another tunnel and go through to a small section of the room which is blocked off from the rest. Go through the door here.
Follow the cage to get a Missile Expansion and head back. When you're back in the Triclops Pit just follow the reverse path back to the little cave; there isn't anything more to find under the floor here. Get back to the ledge where you started, clear the Puffers as needed, and follow the string of platforms to the other door.
Clear the Puffers, then hop the moving platforms to get over the lava. Getting to the middle platform is the hardest part since it's the highest, but it should be no problem if you wait for the platform you're on to be near the top of its range while the middle one is near the bottom.
This is one of the main intersections for the caverns so you'll be coming back here several times. There is a large piece of Space Pirate machinery on an island in the middle of a pool of lava. It's guarded by slightly tougher versions of the Auto Turrets you saw earlier on the frigate, so start by firing missiles at them. There are three of them at ground level, and a fourth at midlevel which won't be in range until you cross the room.
Hop over a stepping stone to a ledge on the left. There is a door here which does not lead to your destination, but there is an expansion in this direction which you might as well pick up now.
There is a slightly damaged enclosed bridge over some lava.
The passage at the start leads to a bridge going sideways over a pool of lava. Jump to the bridge and then to the other side of the pool, timing your movements to avoid the jets of flame coming from the ceiling. The main part of the room is a lake of lava and when you reach it, hop to the ledge on the right, then onto the ledge opposite with a Triclops. Fighting the Triclops here is dangerous because if it grabs you it will throw you into the lava where you'll take significant damage. There is second Triclops on another ledge across from this and the same warning applies, but you will need Morph Ball here so you may want to defeat them despite the danger to avoid trouble coming up.
On the ledge with the first Triclops, switch to Morph Ball and jump into the tunnel. You come out on the other side of the lava lake. Continuing takes you back to Tallon Overworld via the Root Cave, but right now you're here for something else. Destroy the two crates here and follow the Morph Ball Track behind them. Jump up some ledges to a narrow catwalk over the lava. It winds around some and there is no railing to keep you from rolling off, so go very carefully until you reach the end. Jump another level up to a second catwalk and follow it to a Missile Expansion. Drop off the end of the catwalk to land on the ledge where the second Triclops was, then head back to the Monitor Station.
Monitor Station (cont.)
You'll need to defeat the Auto Turrets again so be careful when you enter the room again. Cross the bridge to the island, then bear left and hop over the platform to ledges on the other side. That fourth turret should be in range now so shoot it before it notices you. Scale the ledges going to the left and jump to the catwalk in front of the central structure. Go inside; if you scan the monitors here you'll learn that the Pirates have set up a geothermal station here, because, though they may be crazed megalomaniacs, they still see the value of renewable energy sources.
Cross the bridge to the next door. There is another door higher up but it's out of reach for now and there's not much point in going there until late in the game.
Transport Tunnel A
Follow the tunnel to a Morph Ball maze. You can just scoot along the bottom to the next room for now but there is an Energy Tank here. It's possibly the most difficult one in the game so there's no shame in coming back for it, though you'll probably want to get it before facing the next major boss.
In order to get it you need to do three perfectly executed double jumps in a row; see Missile expansion #10 to learn how to do a double jump. If you haven't had a lot of practice with them then you might want to find a safer place to train yourself up a bit, because if you miss the first jump here you land in a lava and lose health. If your health starts to get too low on this then definitely just continue on to the next save point since it's not that far away now. One of the game demos you get if you turn on the console but don't start a game actually shows Samus completing most of this expansion, so watch that if you're unclear on what to do.
The first jump is on the first crate as you enter the room. One bomb will crack it and two will destroy it, so if you try this jump and fail there will be nothing below to keep you out of the lava. At the top of the jump try to reach the ledge on the left and with a bit of luck you'll get enough of a grip to make it. If not and you fall into the lava, drop a bomb to jump out as soon as you can; you'll probably only take about a third of a tank of damage and with four tanks in reserve you should be able to give it quite a few tries.
Once on the first ledge, go left to the next metal crate. Do the same maneuver again to get to the second ledge. There's no lava this time but if you fail you'll end up at the bottom and will have to start over. Go left on the second ledge to the third metal crate. The third jump is much easier than the other two since you just have to reach the tank; there's no ledge you need to climb onto.
Continue left out of the maze and through the next door.
Transport To Phendrana Drifts North
This takes you to the next new area, Phendrana Drifts
Transport To Magmoor Caverns West
The transport stops here. We've just had the lava level so it's time for the ice level.
This passage is blocked in a few places by walls of ice. Use missiles or the Charge Beam to clear them.
This is a large valley and, as you can see, something of a hub for Phendrana. There are six exits, including the one you just came through.
There are two new creatures to scan here. The first, Crystallite, is easy to find. It's an icy entry in the Zoomer/Geemer/Grizby line. It's ice shell protects it from your beam weapons but a missile will destroy one. They won't attack but they have the bad habit of patrolling the path you need to take.
The other creature, the Flickerbat, is hard to see much less scan. You may spot the light blue trails they make while flying around the pillars in the middle of the valley. They sometimes become visible just after turning, so try to locate where they do this, turn your scanner on, and hope for the best.
The hint system may to pointing to a save station near here by now. It's directly across from where you came in.
Save Station B
Save your progress and scan the walls for clues on what the Space Pirates are up to now.