While wandering outside of any protection zone, you may come across wild Pokemon. They will attack you on sight. Your only protection is using your own pokemon to battle them.
In order to fight you will need to select one of your pokemon from your pokemon roster.
To attack an enemy pokemon you can either use CTRL+left click, right click and choose attack or use the battle tab to select your target.
Your active pokemon will immediately move to attack the enemy you are targeting. So long as you have a pokemon out, your character won't take damage. Defeating enemy pokemon will gain both you and your pokemon experience towards leveling up. Some Pokemon also drop items which can be sold for POKEdollars in the shop.
All pokemon have a list of skills they can use in combat.
Skills can be activated using the skill tab. All skills that the pokemon can learn will appear here, however some skills will be locked until the level requirements are met. You can learn what level the skill can be used in battle by using the pokedex on the Pokemon.
Each skill has a specific cooldown period after it is used before it can be used again. Skills turn red while they are cooling down.
After Knocking an enemy Pokemon unconscious you will be given an opportunity to attempt to capture them with a pokeball. Higher quality Pokeballs with Increase your chances of capturing the enemy Pokemon. Make sure you loot an enemy pokemon before attempting capture. Whether they are captured or not, all Items the have on them will be lost after you use a pokeball on them.