The Temple of Cubos is a facility to exchange Tier Points and Gems for rare gems. It is also used to fight Cubos. These rare gems can be used to buy many valuable upgrades and to customize your tower. You can also buy these with Kreds, which makes them the premium currency in the game.
Factory: You can buy a 1 day, 3 day, or 7 day timeskip with rare gems.
Global: You can buy a Exchange Rate - 20% upgrade and a Special Resource Drops + 50% with rare gems.
Laboratory: You can buy 1 or 5 instant research tokens with rare gems.
You can also buy a set number of gems (depending on your progress the number will be higher) and edit your tower.