After some time, the energy is automatically replenished.
   
You can also get more energy as a reward for some completed quests by doing Bipoto's orders, after leveling up, using an energy altar, by exchanging collections and using energy drinks.

   

As you play and progress through the game, you can also find additional sources of energy, such as an energy source in the form of a Lab reward or by finding various chests in Rescue Expedition locations.