You unlock a Protocol tree with Rank 1; your generic Rank 1 GenPower that gives you an unit or a special power. With this Rank 1 unlock, you can choose to buy the Rank 3 and the Rank 5 power. Rank 5 can be bought independently from Rank 3. The Rank 3 Expansion requires the Rank 3 power, and is generally an upgrade to Rank 1 and 3, but fully optional.
Only Rank 5 are the offensive powers (or in case of Cybernetic Warfare, something similar but still different). There is no limit to the amount of Protocols you unlock during a battle.
The icons and unlocks seen here can still change. If Generals supports it, I might give the Armoured Fist protocol a Rank 5 power.
