In every Operation, Krieger is testing Simulation and Agent variables in certain combinations.

Eventually, every Operation reaches diminishing returns, and Krieger needs to switch up the variables in order to learn more. Thus, ending an Operation requires that all currently running Simulations be reset, and a new series be built.

However, all Agent and Simulation upgrades and bonuses are carried over from Operation to Operation, meaning that when you rebuild the Situation Room in a later Operation, it is far more efficient from the get-go than it was when you built it in an earlier Operation.