Pistol Upgrade
Area 00 -- There are no enemies in this level, so it should be easy to find. Just make sure you enter every open door. Plasma Rifle Upgrade (credit: EngyResurrected)
Area 06 -- At the barrel robot section of the stage, drop off the far right side of the bottom level and immediately grapple left. You'll want to be on the second or third tile, so you may need to retry a few times to get in the right spot. From there, just drop straight down and you land next to a door. Inside is the upgrade. Machine Gun Upgrade (credit: EngyResurrected)
Area 07 -- Don't use the splitter to open the door. Instead, drop down and grapple the ceiling to your right just before you fall to your death. Make your way up along this passage until you reach a door marked with a machine gun panel. Open fire on it with you machine gun to open the door and take your upgrade. Shotgun Upgrade (credit: Kronos174)
Area 08 -- In the first room of the fortress, near the just right of the center, you'll see a small room with a hole on top. To get here, swing into spot left of the blue boxes, then just reel yourself up. To start swinging again, fire your shotgun, and swing up to the room. The upgrade is inside. Splitter Upgrade (credit: EngyResurrected)
Area 10: At the bottom far right shaft, just before you encounter the slimes, head all the way to left, grapple, swing, and then grapple straight up at the top of your swing to grab an easy-to-miss ledge. Next, grapple over to the right and shoot the two blue blocks with your splitter to gain access to the upgrade. Bazooka Uprade
Area 12 - You're given the final upgrade while going through the final stage.