Head right, up, and up the stairs to the deck and save at the silver Mana Goddess so you don't have to go through that super-long cutscene again. Return to the first floor and head south. Kill all the soldiers here. Go back out and head far left and down the steps to the lower-left. The metaball in this room is weak to bash. Open the chest here to obtain a Gumifrog. Go south-east, destroy the window leading outside and jump through. Go east and open the chest to get a Fishscale. Break the nearest window and enter it.
The metaball here is weak to jab. Open the 2 chests here for a Magic Walnut and an Angel Grail. Go down the steps to the left and rush past the eye and enter through any of the doors to the north. Destroy everything in this room to receive Knucks. Go north and destroy all the soldiers in this room. Go back south, down, and up both flights of stairs. Head to the stairs in the upper-left corner and destroy all soldiers in this room.
Go back out of the room, down the steps, and through the first door to the north. Break the window in this room and head outside. Go to the far right and jump down to the platform below and open the chest to get a Sultan Silk. Jump back up and head to the far left and open the chest to get a Magic Walnut. Head right, break the first window and jump through.
Open the chest in this room to get a Round Seed, then jump over the chair and open the chest to get a Spiny Seed. Go down the steps and exit the room. Go through the door in the far north-east corner and destroy all the soldiers here. You should get the key to the control room once the last one is dead. Head back out of the room and go left until you see a set of steps surrounded by 4 walls. Go down these steps and click on the first door you see to open it. Go through the door and follow the path round and up the steps, open the 2 chests for a Chocolump and a Magic Walnut, then go down the steps to the far left. Open the 2 chests in this room for an Oak Wood and a Gum Drop. Save at the golden Mana Goddess, then go down the stairs to the reactor room to meet the Guardian.