At the end of each mission, you get graded, and SS is the highest ranking. The ranking depends on how quick you beat the mission (Total IP), and losses on both sides. Your own losses really cut into your grading, so don't let any of your characters die if you can help it.
You can get the Permanent Will for Nozomu's Aura Shield 2 if you get an SS rank on the first mission of chapter 3.
Walkthrough / Info site:
http://narukana.basci.net/?FrontPage