Supply Points (SP) are the currency with which you build, reinforce & resupply your squad during a mission. The amount of SP you start with is mission dependent; the SP will not carry over from one mission to the next, nor will you receive any reward for unused SP at the end of a mission. Prior to the start of each mission you are told as to whether it is an open or closed deployment, as this will impact on your ability to use SP.
In closed deployment, you can only use your SP for Swapping Templars during the Initial Deployment. In open Deployment, SP can also be spent at Tact Points to deploy additional forces, to buy Ordnance or Upgrades.