TNG - Descent Part I.
Early Trek didn't do 'consequences of our decisions' much. But TNG dipped its toe in the water as it went along, and here we have a full blown sequel to decisions made in TNGs past - specifically in I, Borg. The scene between Admiral Nechayev and Picard where she dresses him down for following his conscience is a very interesting one indeed and opens up so many questions about Federation priorities, the society of the 24th Century, the Starfleet oath and mission, and whether the 'more evolved sensibilities' of our crew are shared widely beyond the influence of Picard himself.
The episode's a bit ropey in places but I love that idea just tossed in there.