Puzzle 1 - The First Chief. Drop all your villagers on the robes in the
amphitheater: any villager except nursing moms can become chief. If you
can't find your chief right away, wait until the moms no longer have
babies and drop them on the robe. (You will need to repeat this process
each time the chief dies.)
Puzzle 2 - The Bee Hive. First, light the fire (collect wood and dry
grass in the firepit, then light the fire). Then drop an adult villager
on the burned out torches near the hive. He/she will return the torch
to the hive and calm the bees so you can collect honey.
Puzzle 3 - The Alchemy Lab. You will need an Adept Scientist (or more
than one). Scattered around the village (random locations) are 2
colored pots (red or yellow with white stripes), a brown pot, a gray
bowl with spoons, and a short spear (orange-brown handle with gray
blade). Drop your scientist(s) on each item and they will return it to
the lab - if they drop the item before reaching the lab, it will warp back to where you found it originally. Returning all five items solves the puzzle.
Puzzle 4 - The Roster of the Dead. At the far right of the map (use
keyboard shortcut '3' to get there) is a grassy area - at the upper
right of this area is a big leafy bush. Have your villagers remove
these leaves, which uncovers the roster of the dead (they will gain
building skill; trained builders can accomplish this faster).
Puzzle 5 - Weather Dancing. You will need Level 2 Leadership, a tribal
chief, and 3 Adept Farmers. First, drop the chief on your lit fire.
He/she will begin weather dancing. Then drop the farmers on the fire,
and they will join in. You will know they are successful when sparkles
appear over their heads and under their feet.
Puzzle 6 - The Lift. You will need 3 Adept Builders and Level 2 Restoration.
Once you have purchased the tech, drop your 3 builders on the "strange
machine" in the orchard. Make sure their action line reads "repairing
the lift". If you have done this correctly, the lift will be repaired.
Puzzle 7 - The Rubble. You will need Level 2 Restoration. Drop a villager
(preferably a builder) on the pile of rocks at the bottom of the map.
He/she will clear away the rocks, gaining building skill (builders will
accomplish this task faster).
Puzzle 8 - The Ancient Bath. You will need to have completed Puzzle 3
and have a Master Builder. Drop your builder on the "chalkboard" in the
alchemy lab (he/she will "see" it if you fly them over the lab) - he/she
will create the the plans for the bath. Drop your builders on the bath
to complete the project.
Puzzle 9 - The Statue. You will need Level 3 Restoration, Level 3 Leadership, a tribal chief, a Master Builder, and a completed bath (solved Puzzle 8). Drop the Master Builder on the chalkboard (which will be blank after the bath is completed), and he/she will draw up plans for the statue. Drag an adult villager (not a nursing mom) up the path to the door until he/she "Sees a good place to anchor the statue" -- this villager is more likely to be successful if he/she has some building skill. That villager will then build scaffolding to help anchor the statue. Your chief must direct work on the statue, so drop him/her on the statue to begin this process - if the chief stops directing work, then progress will halt until you return the chief to his/her duties. Once the chief is directing, you can then drop builders on the statue to help "pushing the statue". The villagers must push the statue up the path towards the door - this will take several hours (you can click on the statue to bring up a timer in the status bar that will help you determine how long is left - but this time depends on how many builders you have working on the project and may increase if builders leave the project). Your builders may occasionally complain that "there is no more room to help out" - only a limited number of builders can work on the statue at any given time.
Puzzle 10 - The Orchard. You should plant your first seed as soon as the game starts: this first seed is located next to the ruined lift: drop one of your adult villagers on this seed and he/she will plant it. To gather the next two seeds, you will need to have completed Puzzle 6 (The Lift). As soon as a rain storm starts, place an adult villager (but not a nursing mom) on the lift (his/her action line should read "Standing on the Lift") Leave the villager there until the lift reaches its highest point, when a seed will fall from the tree above. Drop the villager on the seed to plant it. You will need to plant a total of 3 seeds (the original plus two from the lift) to complete the orchard - the puzzle will be completed once all three trees have become mature (and start producing fruit - it takes about 8 hours on 'normal' speed for the tree to mature). Additional seeds (beyond the first three) will not be planted, but will instead be placed in the food bin.
(Note: If you have trouble getting to the lift before it starts to go up, you may wish to pause the game with the spacebar when you see the rain start before finding a villager. You will need to unpause the game to see their status line to make sure they are properly placed.)
Puzzle 11 - Banishing the Sharks. You will need to have completed Puzzle 3 and have at least Level 2 in your chosen faction, Nature or Magic.
For NATURE: collect the following herbs for a potion: 2 X Black Orchid, 1 x Pitcher Plant.
For MAGIC: collect the following herbs for a potion: 2 X Rose, 1 x Berry.
Have an adult villager (not a nursing mother) drink the potion. He/she will take a vial to the ocean. How the sharks are actually dealt with depends on the faction chosen (the nature potion is a shark repellant, the magic potion "charms" the sharks so they won't bother the villagers).
Puzzle 12 - Aromatherapy. You will need to have completed Puzzle 8, have Level 3 Medicine, and a Master Doctor. Drop your Master Doctor in the completed bath. He/she will fill the bowls around the bath with Lotus plants ("doing aromatherapy"). Then drop a Master Doctor on the fire to light the burners and finish the puzzle.
Puzzle 13 - The Ash Key. Later in the game (after at least one fire cycle - 10 hours on fast speed), you will notice sparkles around the fire. Let your fire go out (do not replenish it with firewood) - a diamond will appear in the ashes. The diamond will be too hot to pick up initially (it was in a fire, don't forget). To cool the key, drop adult villagers on the rightmost of the two waterfalls (where they go to drink and do laundry). They will gather water and drop it on the key. They will need to do this several times (8-10, at least) to make the diamond cool enough to touch - your villagers won't repeat this task on their own, so you will have to make them do it by dropping them on the waterfall. When the villagers no longer bring water to the fire (they'll revert to drinking from the waterfall when you drop them on it), drop a villager on the key - they will take it to the door and solve the puzzle. You will need to repeat this step if they drop the key before reaching the door.
Puzzle 14 - The Hanging Key. You will need to have solved Puzzle 3. Collect the following herbs for a potion: Cactus, Rose, Lotus. Make the potion and have villager (other than a nursing mom) drink it. That villager should feel "light and springy!". Drop them near the pink diamond (the hanging thing) just above the Rose plant - their status line should read "trying to reach the key". They will jump up, collect the key, and place it in the door. If they drop the key before reaching the door, you will have to resolve this puzzle.
Puzzle 15 - The Clam Key. You will need to have solved Puzzle 9. Once the statue is completed, a pearl will appear. Have a Master Builder pick up the pearl - he/she will take it to the waterfall to be "finished", then a master scientist needs to pick it
up and polish it, then have the tribal chief pick up the finished blue pearl: the chief will use the pearl to get the key from the giant clam and will then put the key in the door. (As with the other key puzzles, you may have to repeat parts of the puzzle if the key is dropped before it gets to the door).
Puzzle 16 - The Sun Dial. You will need to have solved Puzzles 13, 14, and 15. Once all three keys are in the door, the sun dial room will be revealed. Drop a villager on the sun dial until it reaches the position at the furthest left (there are three locations for the sun dial). When a beam of sunlight hits the sun dial, ghostly figures will appear in the room. Drop a villager on those ghosts and the mystery of the secret city will be revealed!