Prototype Plans are blueprints used for crafting via the assignment system. They are acquired by successfully completing Secure Prototype espionage assignments.
They can then be used for Deliver Prototype Technology to Allies in Gamma Quadrant (awarding Gamma Quadrant Commodities) or to build Satellite Turrets or Torpedo Platforms via Assemble from Prototype assignments. *just to add ~ you get the plans from being in a "sector" of space, check your "Current Map" on the craftable page, which you will see the craftables for that current area of that space "sector". The blueprints will be different in different areas like at Deep Space 9 you will find Chroniton Torpedo platform prototype plans. This is where the weapon set can be found as well in this area.