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.
One of many wild pokemon you may encounter
In order to fight you will need to select one of your pokemon from your pokemon roster.
The pokemon you have in your backpack can be called using this tab.
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.
Use this tab to select your targets in combat.
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.
Skills:
All pokemon have a list of skills they can use in combat.
Charizards fireball attack wrecking a ratata
Use your pokedex to learn what level your pokemon must be for a skill to become available.
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.
The skill tab.
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.
Catching Pokemon:
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.
Capturing a pokemon using an Ultra ball