I think the technology discovered stolen in part 1 played a big part in the torpedo. However they work as stand alone since it is a Star Trek thing to instantly engineer a work from a base tech.
This commission thing seems to be the season long arc, something almost all the cop genre shows are adding after the 2020 political year. So I think that the blackmail story is just one to keep the commission key members in the viewers sight.
For the franchise I thought it was weird that New Orleans NCIS agents wore their weapon and handcuffs in a different location than the Washington and Los Angeles agents and Agent Carter, was that someone's joke? Since I didn't see last season for the most part I thought he was in the long line of the franchise's agents who find the reason to transfer agencies to NCIS. But he is the other trope. Every squad has an ex special operations soldier on the team, Marine Force Recon in his case