It is based around five Goblin Clans: Stonecrusher, Hellfire, Stormbringer, Plaguespitter, and Nighthorde. The story mode follows the path of the Stonecrusher Chief after the destruction of the mining caves the clan calls home. They then head out to contact the other clans only to find that they've been blamed for the disaster and loss of their master.
Goblin Commander provides examples of:
- Awesome, yet Impractical: The Stormbringer Clan's titan: The Lightning Elemental. It can't disrupt or damage units as consistently as the Stone Ogre nor kite enemies like the Warpigpult.
- Boring Yet Practical: The Stonecrusher Clan's titan: The Stone Ogre. Its attacks are very basic, but it only takes Souls to acquire, which are virtually infinite. 2 of its main attacks work in most situations, and the third allows it to heal itself to stay in the fight longer while taking out a goblin unit instantly no matter how tough it is.
- Crippling Overspecialization: Clan Hellfire and Clan Plaguespitter in general, being so focused on offense they need another Clan to tank the enemy's attacks. Otherwise they won't last long enough to do any appreciable damage. Especially apparent with Hellfire's Titan and Turret, the former of which has no melee attack and the latter of which is made of glass.
- Damage Over Time: Clan Plaguespitter's hat, going with their Hit-and-Run Tactics. They get no defense upgrades whatsoever, instead upgrading their poison weapons and movement speed.
- Developer's Foresight: Some cutscenes change slightly depending on which clan discovers an objective, such as the ruined Soul Foundry in the first Plaguespitter map.
- Glass Cannon: Clan Hellfire's hat. All but 2 of their units are ranged, they forgo a defense upgrade in exchange for upgrading their range even further, 1 being a scout unit that lets them shoot targets that are further away still. In melee, all they can do is hope that their single melee unit can stall the enemy long enough for their archers and riflemen to get the kills.
- One-Hit Kill: Some units such as the Hellfire rifleman have a chance to instantly kill a unit each time they attack. The Stone Ogre can pick up individual goblins and eat them to achieve the same.
- Our Goblins Are Different: They're a Servant Race created by a wizard to create a specific machine.
- Rewarding Vandalism: Smashing rocks and structures in the environment yields valuable gold for upgrades and Titans
- Ryu and Ken: Clans Stonecrusher and Nighthorde. Both have a single ranged unit with knockback and are otherwise melee-oriented with their units striking individual targets for good damage and being difficult to kill.
- Stone Wall: Clan Stonecrusher's hat. Their units are all very sturdy, and their special unit allows them to gradually heal. Their turret in particular is the hardiest turret in the game.
- Tactical Rock–Paper–Scissors: In regards to the Clans. For example, Hellfire has an edge against Plaguespitter, such that a Hellfire team will beat a more numerous Plaguespitter team more often than not. Sometimes the story will have you fighting a Clan you have a direct counter to in this way, as you acquire Hellfire goblins before reaching Plaguespitter territory.