So, I've refined the idea: 

Elise is in Black Ops, a full team of experienced soldiers forming a team of high expertise as they've been tasked with passing off as a NUA squadron. They've infiltrated the comms, gotten IDs, done everything to be as normal as possible, until another Black Ops group attacks their safehouse. Shoot up the place, pursue the escaping Operatives... 

That other team would be a NUA one. Elise of course, escapes and survives until she ends up with the main group, still trying to establish contact with her Black Ops Team.