The HQ is the cornerstone of your base. As it develops, it unlocks new weapons, soldiers and upgrades.
To beat an opponent you have to destroy their HQ. When you destroy other structures on an enemy island, the HQ takes damage too, up to 70%.
Likewise, any opponent attacking you must also destroy your base in order to capture your resources. Build and upgrade defensive emplacements to keep your base well-defended from enemy attacks.