You now have every upgrade in the game, but in order to get to the final area you need to collect all 12 of the Chozo Artifact. They aren't actually useful until this point in the game, so you can get them as they become available or wait and get them all at once according to your preference.
Artifact of Truth
You can collect this artifact after getting the Missile Launcher.
Go to the Artifact Temple in the Tallon Overworld. (See the Missile Launcher page for directions.) The artifact is located under the central statue. Once you have this artifact you can get clues to the locations of some of the remaining ones by scanning the other statues. You'll be able to scan all the statues after getting more artifacts.
Artifact of Strength
You can collect this artifact after getting the Space Jump Boots, though you can save yourself a trip in getting a Power Bomb Expansion if you wait until getting the Power Bomb.
Go to the Monitor Station in Magmoor Caverns. Follow the path up to the second level of the central structure. Proceed as if toward the door to Transport Tunnel A, but just at the end of the catwalk, stop and look up and to the left. There is another platform within reach of a double jump. Jump up then turn around and look up to find a second catwalk. Jump to that and turn right to the third level of the central structure.
Activate the Spinner to lower the collapsible suspension bridge, jump to the ledge beyong the bridge and follow it to the door.
The artifact is on the statue.
Artifact of Wild
You can get this artifact after getting the Spider Ball, but the battle will be easier if you wait until getting the X-Ray Visor.
Get to Sun Tower via Transport to Magmoor Caverns North. The idea is to get back to the Sunchamber, but you can't get there the same way you did when you got the Varia Suit, so you must follow the route you took on the way out.
Clear the Wasps nests so you can explore in peace, then look up at the Spider Ball track to see another gate with four runic symbols. Finding the symbols this time isn't that hard though. First locate the two Cordite wall hangings on either side of the room. Fire Super Missiles to clear them and find two of the symbols. The other symbols are near the tops of two of the four columns around the middle of the room. One symbol is near the Chozo inscription and the other is to the left of the Spider Ball track.
With the gate open you can climb the Spider Ball track, but there are more obstacles on your way to the top. There are gaps in the track and it goes around stone blocks. Drop bombs to jump up the gaps; you destroy a stone block each time in the process but it doesn't matter if you reach the next section of track. Avoid the Oculi circling the blocks because they can knock you down if you bump into one. Continue up the track to the top.
Sun Tower Access
When you enter you may catch a glimpse of a Chozo Ghost. There's nothing else interesting here though.
Chozo Ghosts attack when you step into the room. When you defeat them, the artifact appears in the giant flower in the center of the room and the vines that stopped you from going through the door back to the Arboretum disappear. Jump to the flower to get the artifact, then take your pick for the route back out.
Artifact of Lifegiver
You can collect this artifact after getting the Gravity Suit. It's in the same place as the Wavebuster so you can combine trips if you want to save time.
Tower of Light
Get to the Tower of Light as described on the Wavebuster page. On the way, you may find Chozo Ghosts in the Ruined Shrine by now. Drop into the water and go through the passage at the far side of the room. Jump to the ledge at the end, then go through the door on the ceiling.
The artifact is waiting for you here in a small room.
Artifact of Warrior
Collect this after getting the Power Bomb. There is a boss battle involved this time and you might want to get this before doing the Phazon Suit battle since it will be a good warm up.
Go to Elite Research in the Phazon Mines and drop a Power Bomb near the canister at the bottom. An especially strong Elite Pirate called Elite Pirate Alpha or the Phazon Elite, comes out and attacks. Immediately scan it as it's the only one in the game.
When Phazon Elite has been defeated the artifact appears where the canister had been.
Artifact of Chozo
This artifact is located in the same room as the X-Ray Visor, so you can pick them up at the same time. The Power Bomb upgrade is needed for this.
Get to the Life Grove in Tallon Overworld as you did when getting the X-Ray Visor, or just remain there after you get the visor to save a trip. Drop to into the water and at the center, below the water, you'll find a metal hatch. Switch to Morph Ball and drop a bomb on the hatch there to break it. A pillar emerges with a Spinner at the bottom. Activate the Spinner to lift a metal bridge into place at the top of the pillar. A second pillar rises out of the water with the artifact in a nook near the top. Jump from the nearest shore to the bridge to reach the artifact.
Artifact of Nature
You can collect this artifact after getting the X-Ray Visor. Actually it's possible to get it earlier if you already know where to look, but the visor tells you where it is.
Go to the Laval Lake in Magmoor Caverns, the side near the Lake Tunnel. You may hear the humming of an expansion here which tells you you're getting warm. Switch to X-Ray and you'll be able to see the artifact inside the central pillar. Fire Missiles to break the pillar and jump to collect the artifact.
Artifact of Spirit
For this artifact you need the Plasma Beam.
Get to Phendrana's Edge in Phendrana Drifts and use the Grapple Beam to get near the top. Stop a few ledges short of where you need to grapple the Glider though. Switch to Thermal (not X-Ray) and locate a door hidden behind a stone wall. Drop a Power Bomb to break open the wall and reveal a red door.
The artifact is here among some random Pirate notices. This is one of the few places in the game where the name of the frigate (Orpheon) is given explicitly.
Artifact of Elder
For this artifact as well, you need the Plasma Beam.
Get to the Control Tower in the middle of the Pirate base in Phendrana Drifts. Jump into the chamber above the East Tower and destroy the crates there to reveal an icy window. Fire the Plasma Beam at it to break it open and look through with the scanner. Someone has conveniently left an unstable fuel cell at the base of a tower out there, and even more conveniently it's made of Radion which can be destroyed by a Missile. So fire your Missile to blow up the fuel cell and collapse the tower; it will land on the main part of the room and break one of the walls.
Drop into a hole under where the tower landed, and you'll end up in a gully outside the wall. The artifact is there waiting for you but you can't get back out through the same hole. Instead, switch to Morph Ball and jump into the tower, then roll up through the tower and out the top.
Artifact of Sun
This is a third artifact for which you need the Plasma Beam. Go to the Chozo Ice Temple in Phendrana Drifts.
Chozo Ice Temple
Platform your way to the top level and examine the large winged statue near the exit. It looks like it was a fountain once but the water is frozen. Shoot the plasma beam to melt the ice, then jump into the statue's cupped hands and switch to Morph Ball. This moves the hands and breaks open a tunnel at the base of the statue. Roll inside to get the artifact.
Artifact of World
This is the forth and last artifact for which you need the Plasma Beam. Unlike the other three, this is located in the Chozo Ruins.
Hall of Elders
You been here and have done Chozo bowling before, and now it's time to see what you get when you activate the Morph Ball slot behind the red disk. Shoot it with the Plasma Beam to uncover the slot and activate it. This time there is no bowling involved because all that happens is that the statue slides forward revealing a door in the floor.
The artifact is in this little room under the hall.
Artifact of Newborn
This is the last artifact and requires the Phazon Suit.
Phazon Mining Tunnel
Return to the Phazon Mining Tunnel; the best time to do this is probably right after getting the Phazon Suit since you're already nearby.
Get to the right end of the row of the disappearing floor panels, but instead of continuing out of the maze drop a bomb to break a small barrier on the right. This opens a path through the Phazon with many more similar small barriers; these act as baffles to keep you from getting the artifact unless you have the Phazon Suit. The artifact is at the end of the path.
With all twelve artifacts it's time to return them to the Artifact Temple.