You're nearing the grande finale, but if you're aiming for 100% item collection (which changes part of the game ending), there are some upgrades here in SRX still to collect, and some others throughout other Sectors of the station.
Space Jump back up to the door above and go through. Just Screw Attack through the Rippers to kill them, and exit right. Make your way to the Save Room at the top of this shaft, then go back down to the upper-right door. Go through.
Use a Power Bomb to destroy the barrier to the right, then go through the open door on the right. Screw Attack the Space Pirate here to destroy it instantly, then bomb the floor to the right to reveal the ladder leading down. Head down it, then go through the narrow passage to the left and grab onto the ladder below. Shoot a Diffusion Missile against the wall to open a passage to the door to the right. Pull into it and roll through it, and exit.
Shoot through the gate at the light to open it, and exit right. Screw Attack through the thin floor in the middle, head down and Screw Attack the Space Pirate to kill it. Pull up into the gap to the right and fall below, and go through the door here. Screw Attack above the block with the red thing on it to break it open, and roll through it. Screw Attack your way through the Rippers and walls to the right, and you reach a wall with a gate against it. Screw Attack the wall to open a gap, then shoot through to the flashing light and grab onto the gap to roll through and exit right.
Screw Attack your way up, killing the Space Pirates for extra energy, and Screw Attack through the platform above. Go through the door on the right. Just continue on the straightforward path until you fall through some Pit Blocks (you'll notice the outer shell of a Metroid on the way). Use the door at the bottom here, through a room with a couple of Hornoads, to reach a Save Room. Save, then get against the left wall and make a running start to the right while shooting. Once you reach the SR388 environment room with the ladder going down, press down before reaching the edge to hold the Boost energy. Jump diagonally to Space Jump (without Shoulder Charging) down through the narrow gap to kill the Scizor below, then get against the right wall (all the way against it) and do a Hyper Jump straight up through some Boost Blocks up above (keep trying; it took me a million tries to get it right). Hold left to grab the ledge so you don't fall back down again. Shoot the left wall to reveal a Power Bomb Tank. Grab it, and return to the Save Room.
You will want to Speed Boost to the right again the same way you just did, but this time crouching in the room right after the two Hornoads (you will Speed Boost about halfway across the room). Space Jump up to the door above, shoot it open, then do a Hyper Jump and press left to Boost through the door. Hold left and you will continue to run in a Speed Boost towards the left. Before reaching the depression in the floor, crouch to hold the energy, then get against the left wall and Hyper Jump straight up to get through some Boost Blocks in the ceiling (again, it took me a million tries). Collect the Energy Tank here, then fall back below and exit through the top right door.
Keep going until you reach a shaft with platforms you can Screw Attack. Save in the Save Room through the top right door, then go back to the shaft and through the door across from you. Then Screw Attack up to the first door on the left. Continue left to reach a room filled with lava. Space Jump to the top left corner of the room to find a Missile Tank. Then fall below into the lava (the Gravity Suit protects you from it), and at the bottom head right and roll into a ball and through the hidden passage to a Missile Tank.
Go back through the passage and to the left through a green hatch. Space Jump up, Screw Attacking through a barrier above (and seeing another outer shell of a Metroid) and go through the blue hatch above. Now you're back at the very beginning of the Sector. Go through the green hatch at the top right of the room and Screw Attack through the ceiling to find a Power Bomb Tank.
If you want to collect the rest of the upgrades in the station, don't go to the Navigation Room yet, because Adam will close off all of the Sectors in the station. Once you do beat the game, the Sectors will all be open again, and moreover, a feature will be added to your map screen showing how many of the total upgrades in the game you have collected (of course, you will start over from the beginning). If you have found all of a certain type of upgrade in a Sector, that type of upgrade's icon will appear at the top with a check mark next to it. This will make it easier to find what you're missing.
As stated earlier, part of the game ending changes depending on whether you've collected everything or not. If you go ahead and finish now, before collecting everything, then you get to see a different thing first. You will then will be allowed to beat the game again, collecting everything beforehand, and see another ending. Also, there are different endings for finishing in under 2 hours, and under 4 hours (and each of those is different depending on whether you've collected everything). But once you beat the game, a game clock will also be added to the map screen to help you achieve those goals (and the new map features will remain if you start a new game in this save slot). So it's up to you.
To collect everything now in the shortest amount of time, head back to the first room of this Sector and go for the blue hatch at the bottom left. In this room is a hidden passage in the wall left of the blue door, so jump against the wall to grab hold and pull up. Screw Attack through the barrier to the left and go through the hatch. Go through the outer-space tunnel to Sector 3.
Sector 3 (PYR)
Screw Attack through the wall here, then Screw Attack through the floor. Clear the corridor of enemies and open the hatch at the left. From the hole in the floor make a running start towards the left, crouch before going through the hatch, then jump and press left to Shoulder Charge through some Boost Blocks in the next room to the left. In the room you reach, drop a Power Bomb to open a tunnel towards the left. Go through it to get a Power Bomb Tank. Return to the last little room and Screw Attack the bottom-left corner to fall below.
From the first room of this Sector (reached by exiting left from this room), use the second door on the left to a room filled with lava. Make your way across (Space Jumping might be faster than using the rungs, or even just walking through the lava, but watch out for spouts) and go into the room beyond. Screw Attack the left wall to break it open. You should have gotten the Energy Tank from this room. If not, from the hatch, run to the left while shooting to break the blocks in your way so you can Speed Boost. Before hitting the wall, crouch, then walk against the left wall and Hyper Jump up through the Boost Blocks in the ceiling. Space Jump to the Energy Tank above.
Drop back below. To the right of the hole in the ceiling, part of the floor is made of Screw Attack Blocks. Use a Power Bomb to find them if you need to. Fall through them, then use the hatch you find to the tunnel to Sector 5. Use a Power Bomb out here to reveal a Power Bomb Tank. Then return to Sector 3.
From the first room of Sector 3, use the bottom right door. Get up on the platform and kill the Fune/Nahime with a Screw Attack, and fall through the Pit Blocks in the floor where it was. Open the gate, and from the hatch run towards the right. In the next room you will break through some Boost Blocks in the floor. Walk left to fall through a Pit Block, then use a Power Bomb below to open a passage towards the left. Pull into it and roll through. Kill the Fune/Nahime quickly with a Screw Attack, then Space Jump up to the Power Bomb Tank.
Get to the tall shaft with all the Funes/Nahimes, and get to the bottom and use the bottom-left green hatch. Cross the lava to the next room. Use a Power Bomb to break a hole in the floor. Drop down to a sort of maze in the lava. Fall lower down and head right but stop short, because the floor to the right is made of Pit Blocks. Jump onto the ledge to the right, jump through the ceiling and continue right. Follow the path around the room counter-clockwise through some hidden passages to reach the Power Bomb Tank you saw at the beginning.
Back in the tall shaft with all the Funes/Nahimes, use the bottom-right green hatch and continue right to reach a big room with lava in it. Shoot the gate open and jump into the lava and head right. Screw Attack through all the blocks of the wall here to clear a path. Get to the left side of the lava pit and start running right while shooting to Speed Boost into the next room. Before the right wall, crouch to hold the Boost energy, then get against the right wall and do a Hyper Jump up above. You'll get a Power Bomb Tank on the long way up.
Drop back down the narrow shaft you just flew up through and hold left to land in a gap. Screw Attack through the ceiling here, head left and Screw Attack the floor to reach the Power Bomb Tank. Space Jump back up through the narrow shaft to the door above. Go through this corridor, then Screw Attack through the wall in the next room. You're done sweeping this Sector for upgrades. Screw Attack through the ceiling and the wall to the right above to get back to the tunnel to Sector 1.
Sector 1 (SRX)
Your goal is the tunnel to Sector 2. Make your way right into the big room at the start of the Sector. Go up and through the green hatch at the top right. Screw Attack through the ceiling, then jump against the right wall above to grab a ledge and pull through. Go through the hatch here and through the tunnel to Sector 2.
Sector 2 (TRO)
Screw Attack through the wall and the enemies in this room. Go right twice to the big first room of the Sector. Head through the top-right door, go right again, and up into the Security Room via the blue hatch. Screw Attack against the left wall near the ceiling to break through to a hatch. Go through it.
If you set off a Power Bomb in here, you see that most of the platforms are made of Pit Blocks. Space Jump carefully (and rapidly) to the top-left of the room, avoiding the platforms (it's hard; keep trying), to get an Energy Tank. Then Space Jump back over to the right, down under the Pit Block platform, and to the left to get a Power Bomb Tank. Head right to fall through the Pit Blocks, then walk right and Space Jump up at the end to get to the hatch back to the Security Room.
Screw Attack back through the wall to the right and head out of the Security Room through the blue hatch. Exit this shaft via the door below, and exit this corridor to the left to get to the big room at the start. Go down past the blue hatch, then jump up into the narrow tunnel just below the hatch and roll through it. Exit right to a tall shaft, and fall all the way to the bottom and exit left. Screw Attack through the top block in the floor and destroy the one below it with a Power Bomb. Exit right to a Save Room. Go through it, then exit right again, then fall below to the hatch leading to where you fought Zazabi.
Space Jump to the top right corner and Screw Attack the wall to the right to get to a hatch. Go through. Fall below and set off a Power Bomb to uncover a Missile Tank blocked by Boost Blocks. You will have to start running from the right, crouch before the left wall, then Space Jump up, shoot your beam to stop Space Jumping, then press the jump button when you're in line with the Boost Blocks, and hit right to break through them and reach the Missile Tank.
There is a Power Bomb Tank up above, and you must chain together some Shoulder Charges to get it. It's extremely tricky; keep trying, and don't be too hasty. From where you collected the Missile Tank, run to the right and crouch before hitting the right wall. Space Jump to the platform above, then Shoulder Charge to the left and you'll hit the ramp running. Before hitting the wall, crouch, then Space Jump to the platform above, and repeat the process until you reach the top of the room, hopefully still Speed Boosting. Before you hit the step to the left, crouch, then Space Jump onto the step. Shoulder Charge to the left and you should hit a ramp and continue to run left through some Boost Blocks to a Power Bomb Tank. Fall through the Pit Blocks to the left and exit through the hatch.
In Zazabi's room Screw Attack through the left wall, then Space Jump to the hatch at the top left and go through it. Jump to the chamber above, and exit left through the hatch. Exit left to the Save Room, and keep going left until you reach a door destroyed by the SA-X. Screw Attack through the floor to the right of it to reach a room where you saw an SA-X, head to the right of the tunnel and Screw Attack through the floor at the right to get below. Exit left to reach a tall shaft. Drop to the bottom of it and exit left, jump and roll through this corridor with the Puyo and exit left again, then make your way to the hatch at the top left. Go through. Jump up to the hatch above and go through to another tall shaft. Space Jump and roll through the narrow tunnels to get to the very top, then crouch on the platform and shoot the wall to the left to open a block. Roll through the gap and Space Jump to the Missile Tank above. Now you've collected all you were missing in Sector 2. Unfortunately, because of the door an SA-X destroyed in a chamber nearby, you have to take a long, circuitous route to the tunnel to Sector 4.
Go through the tunnel to return to the tall shaft, and make your way back down through the narrow passages here to get to the hatch at the bottom. Go through, drop below and go through the bottom hatch. Make your way to the hatch at the bottom right and go through. Continue through this corridor with the Puyo to the hatch at the right and go through. Climb all the way to the very top of this shaft and exit through the door at the top. Exit right through the small room, then jump above and roll through the tunnel at the top left. In this big first room of the Sector, exit through the door at the top right, go through this corridor and exit right, then Screw Attack the right wall to reach a hatch to the right, which leads to the tunnel to Sector 4.
Sector 4 (AQA)
There should be no upgrades to collect in Sector 4, so Space Jump up this shaft and Screw Attack through the ceiling above, Screw Attack through all the puffer fish on the way to the top of this shaft, then once on the ladder at the top charge up a Diffusion Missile and fire it above you to destroy some Missile Blocks. Ball Jump against the right wall to go through a hidden passage to find the hatch to the tunnel to Sector 6.
Sector 6 (NOC)
Screw Attack through the wall here, jump above and exit right. Screw Attack through the wall straight ahead to the right and exit through the hatch at the top right of this dark room. Go through this corridor and exit right to a shaft. Head to the second hatch on the left and go through. Go to the far left of this corridor (Screw Attacking through a block in the way) and start running right while shooting to get back to the last shaft. Once in the shaft, crouch, then jump and press right to Shoulder Charge through a bunch of Boost Blocks to a hatch. Go through it.
Before doing anything else, turn around and shoot open the hatch behind you. Now, if you go to the far right you see an Energy Tank (which should be the last one you need) but it's actually blocked by Boost Blocks. There appears to be no way to Speed Boost through to it, but there are actually metal elevators between the holes in the upper floor that will go out vertically if you bomb certain spots on the platforms. There are some elevators that go up horizontally, though, which will block your path to the Energy Tank. If you accidentally set off one of those you'll have to leave the room and come back in to reset them. The places to bomb are the middles of the two longer platforms and the medium length one, as well as the edges of the small platform. Once you have a path to Speed Boost across, start running from the left, then when you get to the end Hyper Jump through the blocks in the way of the Energy Tank.
There is still a question of getting out of here, because those Boost Blocks in the last room will be there again. Shoot open the hatch out of here if you didn't already, then start running from the right. Before you fall down the step, crouch and Shoulder Charge left through the door to break through the blocks in the next room.
Go through the hatch you should have just collided with, and Screw Attack the block in the way once again, killing all the enemies along the way. Shoot open the red hatch at the left. Go back to the right and start running left, then crouch when you Speed Boost and Space Jump onto the ledge by the hatch you just shot open. Jump and hit left to Shoulder Charge through the door. You will break a bunch of Boost Blocks and reach a big room, passing a Power Bomb Tank on the way.
Jump atop the platform above, run to the right, then run back left so you Speed Boost. Crouch before you fall, then Space Jump left to drop below. Shoot your beam to stop Space Jumping, and Shoulder Charge to the right just when you are in line with the Power Bomb Tank (one block below the ones you destroyed). With luck, you'll Shoulder Charge at the right spot and get the Power Bomb Tank.
In this same room, fall below to the bottom. Go towards the very bottom left, then run back to the right to Speed Boost. Before hitting the wall, crouch, then Space Jump onto the ledge above. Jump and Shoulder Charge left to hit the ramp running and BEFORE you hit the bridge start Space Jumping left and up (don't crouch first). You should be moving pretty fast; try to get up as high as possible. After your second bounce in the air let yourself drop and you should fall through the "roof" made of Boost Blocks below to reach the Power Bomb Tank. Once you get it, Screw Attack through the floor to the right and you'll fall through some Pit Blocks below. Now simply Space Jump to the hatch out of here. There is a Pit Block at the end of the tunnel up above, so roll through and fall through it. Still as a ball, roll through a hidden passage to the right and you'll be out.
Exit through the hatch to the right of the Puyo into the next room (where you fought the Security Robot). Screw Attack over the block in the floor (made of Pit Blocks), through the two walls in the way to reach a hatch. Go through it. A Power Bomb will reveal a Power Bomb Tank, a tunnel above, and Pit Blocks between you and the tank. This is another that is hard to get, so be patient and keep trying. You need to roll through the tunnel, then as you reach the Pit Blocks tap up twice to stand up then try to Space Jump up to the corner with the Tank. With some practice you'll get it.
Almost done with upgrade collection. (If you're like me you're sick of this intense background music at this point.) Your last stop before returning to Sector 1 is the Restricted Zone, accessible from Sector 6. From here, Screw Attack through the bottom left of the floor to get into the corridor below. Exit left to where you fought the X-infected Security Robot, then continue to the hatch at the left and go through. Go down below and exit left. Descend to the bottom of the shaft with a Screw Attack through the floor on the left, and go through the red hatch to the entrance to the Restricted Zone. Shoot through the gate and roll through the tunnel.
Fall through the Pit Blocks at the end of the tunnel and go through the red hatch to a Save Room. Once you exit the Save Room to the left, start running left while shooting until you reach the tunnel out in space. Crouch, then center yourself in the tunnel (behind the second "band" around the tunnel in the foreground) and Hyper Jump up to get a Power Bomb tank in space. You will jump up into the tunnel above where the Restricted Lab was, leading to a Navigation Room where you will be forced to uplink.