On the left side of the Tower Lobby is a set of stairs. Instead of going up, walk past them and you will find yourself in a little space under the stairs. The first gem waits inside.
In the Laboratories, there should be glass tubes near the right entrance. Inside the larger one is the second gem. You will have to grab a balloon from the left side of the room and float into the tube.
The Garden isn’t exactly thriving. Grab the bucket and fill it with water, then water small plant in the lower end of the area. A flower will grow, and the third gem will be exposed if the flower is hit with a bright light.
Once the water is running in the Botany Lab, grab a bucket and fill it with water. Walk over to the small plant in the back of the room and water it to grow a flower with the fourth gem inside.
Now in the Seedling Laboratory, grab a hold of the nut launcher and aim for a mouse with the fifth gem on its tail. Once hit, the gem will plop onto the floor.
In the Tower Lobby, on the right wall, use the Dark-Light Device to uncover a hidden door. Before entering, head up the stairs and restore the two water pipes with the Dark-Light Device. Enter the door and a plant on the left side should grow a spiked ball. Suck it up and throw it at the venus fly trap. Once defeated, open the treasure chest with the sixth gem inside.
Once you have access to the web balls in the Hollow Tree, grab one and light it on fire. Go down the left corridor and burn through the spider webs. Grab the bucket and fill it with water. Head down the right corridor and water the plant there. A flower will grow with the seventh gem inside.
As soon as you reach the Old Graveyard, look up and you should see the eighth gem hanging from a tree branch. Suck it down and it’s yours!
During the fourth mission, head to the Skybridge. Now overrun with flora, make it to the end where an orange flower enemy waits. Defeat it by sucking it down, revealing the ninth gem in the process.
In the Rumpus Room, run around the creepy doll until the head unscrews and pops off. The tenth gem waits inside.
On the bottom floor of the Solarium, use the Dark-Light Device to reveal a hidden treasure chest. Inside is the eleventh gem.
Make your way back into the Conservatory and ride a balloon up to the platform on the right side of the room. Use the Dark-Light Device to reveal a hidden door. Upon opening, Luigi will be transported to an alternate dimension where he is tasked with collecting all the Red Coins in the room before the time runs out. Doing so will reward you with the twelfth gem.
The West Bathroom is the home of the last and final gem of Haunted Towers. Run over to the toilet paper and give it a good tug with your vacuum to let the tenth and final gem fly out.