After climbing up from the manhole, there is a save point that you can use. Run inside the first train car on the right by use of the metal grate. Run through, exit near the barrel and search around the barrel for a Hi-Potion. Now go back towards the manhole and climb the train using the ladder. There is a Hi-Potion on top of the car that you can retrieve. Then continue until you reach a large metal beam, which you can hope onto. Once on it, you can climb down to the left. Check around the barrel to the north for an Echo Screen. Circle around right, then down until you are at the door of the next train. Enter the train and get the Potion. Go down and exit to the right. Go across to the ladder on the third train. Climb across, and down the other ladder. Go up and enter the train. Go up, and exit the train. There is a Potion at the top of the screen that you can get.
Go up and around the train car on your left to get the Potion. Go up and around the next train car to the left and search around the barrel for an Ether. Now go up and all the way right to the engine. Get in the engine and it will push the car out of the way. Climb back in the engine again to back it up. Run and get in the other engine to the north causing it to move also. Get out and climb the ladder on the adjacent car, get the Hi-Potion, and climb across to the left. Climb down from the train, and head left, towards the AVALANCHE Hideout.