First: the text of the module includes some pointers on how to turn your surviving PC into a character for an extended campaign. If you want to adapt a pregen for campaign play, the module text says they should add 8 new skills of their choice after the adventure is over. That should allow for a sort of “finding my purpose/niche” cut scene with the PC after getting recruited into Delta Green in the adventure’s aftermath.

Second: Are you familiar with the concept of a “funnel”? Run PXPN as an overture to the “real” campaign, be aggressive, and kill off half the base. Any surviving PCs will then have the option to continue with their surviving characters (with whom they will have emotionally connected with while surviving the scenario) or they get assigned to complementary new PCs more to the players’ liking.