The Agency was a secret corporation that hired agents to engage in secret missions, such as working against villains. Clank was a member of the Agency.
The Agency manufactured weapons and gadgets that were hidden in seemingly innocuous things such as bow-ties and watches. The Agency also manufactured Proto Weapons, which were upgraded versions of their normal weapons.
The Agency's products were not free. Even its own agents (such as Clank) were required to purchase them if they wished to use them.
It is evident that Gadgetron supplies ammo for Agency weapons, as ammo (except Blackout Pen ammo) is stored in the blue Gadgetron ammo crates that are seen in Ratchet & Clank: Size Matters.