If you explored the MIDDLE LEVEL but missed the crowbar or the CROWBAR that opens the door to secret #2, you can go back for them. The secret is optional, but you must have the CROWBAR in order to get the LEAD ACID BATTERY so you can finish the level. At the JUNCTION, return to the MIDDLE LEVEL MINE CART and get in. Then follow the main walkthrough for that section. You'll find the CROWBAR and the button in the CAVERN WITH THE POOL AND SNOWBANKS.
If you missed the crystal on the LOWER LEVEL MINE CART TRACK, get back in the cart and ride around again. Ride up the slope, ducking under 2 girders. The switch at the top is already in the correct position to shunt the cart off to the left. Duck under the girders but don't brake between here and the pool where you stopped before. Get out of the cart and back in. Duck under the girder, then brake for the curve. Duck under the girder near the top of the long hill, then quickly stand and smack the switch that you missed earlier and continue straight on to the crystal and back to the lower level of the JUNCTION.
If you arrive at the POOL WITH THE WINCH AND YELLOW SUBMERSIBLE and you're missing the LEAD ACID BATTERY or WINCH STARTER, you'll need to go back for them now. You can also go retrieve the first 2 secrets if you missed them.
Get into the mine cart and ride back to the JUNCTION. On the way, you'll encounter several hazards: Duck under a girder as you ascend the first hill and a second girder on the downhill. Don't brake or you won't clear the gap in the track just beyond the second girder. As soon as you cross the gap, stand up and brake hard to avoid derailing on the next sharp curve. Then hit the switch just ahead to go straight. (If you miss this switch, the cart will continue right and crash into the wall.) Do not brake after the switch in order to jump the next gap. Then duck under 2 girders on the way up the next hill and a third girder just around the curves at the top of the hill. As you pass the metal support column, get ready to whack another switch, which will send the cart off to the right. (If you miss it, the cart will continue straight ahead and crash into a hole.) Beyond this switch, duck under a girder and jump another gap. Then, as you pass under a red light, immediately stand and brake for the next sharp curve. Duck under 2 more girders as you head down the final slope to the JUNCTION, where the cart will stop automatically.
Once you're back at the JUNCTION, you'll need to re-explore the other side areas to get the battery and/or winch starter.
If you have the CROWBAR but are missing the BATTERY, you just need to go to the padlocked door on the middle level of the JUNCTION. You'll find the battery inside. (screenshots)
If you don't have the CROWBAR or the BATTERY, follow the walkthrough for the MIDDLE LEVEL MINE CART here.
If you don't have the WINCH STARTER, follow the walkthrough for the LOWER LEVEL MINE CART here.
You can also go back for the first two secrets. Secret #1 is on the upper level of the JUNCTION AREA. Secret #2 is right next to secret #1, but in order to access it you must press a button in the same area where you find the CROWBAR.
Once you have everything, ride the UPPER LEVEL MINE CART back to the POOL WITH THE WINCH AND YELLOW SUBMERSIBLE and continue on your way.
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