As soon as Alundra enters the Coal Mine, a cave-in causes the left exit to the room to be blocked, use a bomb to destroy the blockage then go through the newly opened exit. In the next room, ignore the lever behind the locked gate for the time being, but keep in mind where it is, head to the top left, using bombs to kill the turtles and then to break through the gray rock floor. Head down the stairs, in the next room, go right and up into the shallow pool, killing the Murgg once they attack. After that, talk to Lyman, who gives Alundra a key. The four chests along the back contain, from left to right, Herbs, 30 Gilder, Herbs, and 30 Gilder.
Head back to the start of the Coal Mine and head through the right door, unlock the gate using the key and hit the levers there in the following order: Left, left, right and left. This starts the engine and allows Alundra to use the Mine Cart, hop in the mine cart at the entrance and ride it, once it stops, take the left door and go up the stairs, watching the falling rocks block the route to the switch and opening up an another route.
Now take the right door, coming to a miniture maze in the pool, the two possible routes are shown on the map to the left, the blue route is longer but the falling rocks have a longer gap in between each one, while the red route leaves no room for error but is much more shorter and faster. Jump up the wooden structure, being careful to dodge the falling rocks, hit the lever in the next room and head back to the room containing the mine cart.
Head down at the T-junction and head left, hitting the lever, before getting into the mine cart again. Once the cart finishes moving, jump down onto the lower floor of the room, kill the turtles and slimes, hitting the lever at the bottom-right of the room, this opens a door to the right of the mine cart. Jump back up (using the baskets as stepping stones) and go through the newly opened door. In this room, kill the Murgg and then talk to Jaylen, finding another key in the process. Get back in the mine cart, hitting the lever in the room Alundra finishes at, before getting in the mine cart again, ending up back at the start.
Head through the left door and hit the lever previously barred by the gate, getting in the mine cart once again, ending up in a new area this time. Use the key to unlock the door to the left of the mine cart. The purple glowing tile near the middle of the room leads Alundra to a room where he can save his progress and restore his health and magic. Go towards the bottom left of the room and into the shallow pond, using either a bomb or dagger to hit the lever, causing a block to fall on one of the platforms. Head back and jump on the mine cart just above the two gray rocks, jump onto the wooden structure, and then to the rock on the right, pushing it onto the lower one, destroying both of them. Push the mine cart through the new route and jump on it, and then onto the wooden structure above Alundra, from there, jump to the left one and open the upper chest, which contains herbs, and then the lower one which contains herbs. Jump back onto the mine cart and head downwards, heading onto the stone block and then through the door on the left. In this room, bomb the grey area of the floor and jump down the hole.
In this room, use the stakes as stepping stones and go towards the top right of the room. Talk to Zane and then open the chest, which contains a key, go back two rooms and use the key to open the gate at the right of this room. Hit the lever and then jump in the mine cart. Once Alundra stops, go towards the right of the room and pick up one of the two crates on the left, allowing access to the wooden structure. From the left of it, jump down onto the cliff at the bottom of the room. Jump off the left side of the plateau and follow the wooden structure, using the steps to the left of the mine cart to get up to the top of it. From there, jump up the two steps and jump onto the raised area to the left, the chest there contains a Gilded Falcon.
Exit through the top left of the room and head up the other wooden structure, the chest on the left containing herbs, jumping across to the other one to jump into the mine cart. Hop up the wooden steps, go up the stairs and out of the next room through the exit. In this room, go down towards the engine, and read the sign, which says to hit the bottom lever three times and the top lever once. Do this, and then jump on the main engine three times, at which point it should begin working. Jump onto the gray tiles and ride the elevator down, walk into the blue sparkles to restore Alundra's health and go down into the final room.
Watch the short cutscene with Zazan and then kill the Murgg there, opening the chest, which contains a Life Vessel and then exiting through the south of the screen. Rocks will prevent Alundra from re-entering the Coal Mine, go left, following the Murgg up the stairs and entering the Great Tree Tower. A short cutscene will play showing the area. Head back South and then to the East, walk down to where the grey rocks were and talk to Kline, Meade and Jess.
After they leave, head South to the small circular grey rock, and jump to the right onto the raised cliff, head further to the right and open a chest containing a Gilded Falcon. In order to get back to Inoa, head South one screen, heading right over the bridge, and then North as soon as possible. Go through the East exit and then South to get back to Inoa.
Head towards Jess' house, where Sierra will tell Alundra to see Sybill, head to Sybill's house and talk to her, answering yes to her question and watching the dreams. After that head back to talk to Sierra and then enter Jess' house. Jess gives Alundra a bouquet of flowers to place on Olen's grave. Leave the village and head North into the Cemetery, standing in front of the top right gravestone. Alundra will pay his respects and then the screen will darken and a voice will call to Alundra. Head to the Northeast of the Cemetery and touch the glowing light, entering Lars' Crypt.