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In general game automatically calculates exact stats for the enemies. It takes enemy default values and applies modifiers to make them stronger, normal, or weaker.
How are modifiers created?
Each level has a field called Required Upg (configured here). It is an approximate amount of upgrade you want player to have to experience normal difficulty. If a player has more upgrades than required enemy stats will be nerfed and they will feel easy to beat. If a player has fewer upgrades than required, enemies will feel stronger.
Into account are taken upgrades of the weapon and upgrades of the character itself.
To “explain” the game how you’d like the player to progress and what approximate upgrade you’d like to have at a certain level you assign a Key Upgrade Number field in Weapon and Character upgrades, meaning at level 2 I would like the player to have upgraded Minigun and at level 3 requires an upgrade of the character. Even if the player doesn’t exactly follow your expected sequence (upgrades something else) it still counts - the Key Upgrade Number just tells the game how strong on average you want the player to be.
Balancing
To start balancing the game you need to come up with the “normal” difficulty. Set up the enemy, weapon and character stats without any upgrades so it feels fine. You should playtest it with different enemies and with different combinations of characters and weapons.
When you’re happy with how it feels you can start balancing the progression. By controlling the prices of upgrades (here) + the amount of coins players receive by level completing (here) + the required amount of upgrades (here) you can build the required feel of progression.