Going into the last couple episodes of season two, they had rather a lot of balls in the air, but they tied up the loose ends and landed the plane quite nicely, with a bit of a twist at the end and room left to pick up where they left off with further adventures should the opportunity arise.
Grade A storytelling. It helps that Joe Barton wrote all sixteen episodes, so there wasn't any of the unevenness or style differences that can sometimes happen in more conventional series.
.