US Navy plans self-building floating fortresses
Swimming, stacking ISO containers: Just add SEALs
But normal warships are ill-suited for such jobs, being designed for high-intensity warfare against high tech enemies. They can make a useful effort at disaster relief, and a less useful one against pirates or blockade-runners, but they are so expensive and thus so scarce it's difficult to get much done with them.
Thus TEMP, which seeks to deliver effective sea power using humble container vessels rather than hecamillion- or multibillion-dollar purpose-built warships.
Firstly, there will be a relatively normal effort to create a snap-together instant ISO-box kit which would turn the host ship into a useful platform.
The right mix of ISO-sized modules would then allow a conventional containership to be temporarily acquired and staffed for a useful military function which relieves the burden on conventional force structure. A certain set of modules would be required for any TEMP mission, such as military communications, command and control, expanded habitability functions, expanded power generation, damage control, and self-defense / force protection. Another set of modules would be mission specific, allowing the ship to be converted to a platform capable of accomplishing a specific mission, such as HA/DR or maritime domain awareness and interdiction operations.
This much has more or less already happened. The British fleet at least is already well accustomed to carrying out various military tasks using (often temporarily) modified merchant ships. Sometimes these ships are in regular Ministry of Defence service as Royal Fleet Auxiliary vessels, but sometimes they are just hastily converted merchantmen, as happened in many cases during the Falklands War.
But having a ready-made ISO container set all ready to go would be very handy. A set of modules could be kept parked up on road trailers, ready to be hauled out to a container port and swiftly put aboard ship for deployment. As DARPA points out, some would be standard for every job: comms shack, command cell, living quarters, power and so on. Others - perhaps pop-up weapons stations, UAV or aircraft hangar/pad units etc - would be added depending on the job.
A fleet of cheaply-chartered container ships kitted out with helicopter-pad and marine boarding team units would be able to fight the pirates of the Horn of Africa far more cheaply and effectively than frigates and destroyers can, for instance.