Unit Upgrades are available when the Megastage's technology level is reaches level III. Upgraded units have higher health, do more damage, have more effective buffs and debuffs, and have more powerful double team abilities.
Units can be upgraded in the same menu from which they are hired. This will upgrade all existing units and any new units of that type for the duration of the stage battle.
- Main article: Coil Hierarchy
Upgrading works differently for the Tainted Coil: Only hierarchy units (Battle Nuns, Warfathers, and Overblessers) are constructed through the stage, whilst all other units are summoned through the hierarchy units . Hierarchy units are capable of summoning an upgraded version of lesser hierarchy units, which can summon upgraded versions of their own units. For example:
- The default Battle Nun can spawn a squad of Soul Kissers or a Punishing Party, and they would be considered "level 1". This cannot be upgraded, a level 1 Battle Nun will always spawn level 1 units.
- A Warfather can spawn his own units as well as a level 2 Battle Nun, who in addition to being more powerful than a level 1 Battle Nun, can spawn level 2 Soul Kissers and Punishing Parties, who are more powerful than their level 1 equivalents.
- An Overblesser can spawn a level 2 Warfather, who can spawn a level 3 Battle Nun, who can spawn level 3 Soul Kissers and Punishing Parties, who have almost twice as much health and power as their level 1 counterparts.