It would be asking a lot for the writers to wrap up everything started in the first season, when they were clearly focused on setting up and then executing a mid-season linkage to a feature film.  Make no mistake; that has basically never been done, so it took a lot of planning to pull it off well.  Not only has every episode since The Winter Soldier been a follow-up to the Hydra reveal, but this season finale serves as the direct next step for SHIELD as a whole in the Marvel Cinematic Universe.

That doesn’t mean that a lot was left on the table; just that some plot points best left unresolved and further explored are still open for the second season.  But the major arc for the first season is complete.  Garrett, aka The Clairvoyant, has been eliminated.  Mike Peterson is now free from Hydra influence, even if his life will never be the same.  Nick Fury explained himself to Coulson (as much as he ever does) and provided the seed for the resurrection of SHIELD as it should have been from the start.

What’s left?  Well, the very end made it abundantly clear that Coulson is not entirely himself, which ties back into the discovery of alien writing earlier in the first season.  Skye’s father is known to Raina, and I still feel as though her origins will tie into the Coulson mystery before all is said and done.  Quinn and his plans for Graviton are still up in the air, and Ward is now in custody, so both of those items are likely to return before long.  More immediately, I suspect we’ll see what will happen with Fitz, since it would be weird for him to survive yet be taken off the board completely.

The effect of GH325 on Garrett was unusual, leading to the instability that left him vulnerable in the end, but it was also a clever way to foreshadow what was going on in Coulson’s head.  If this is what the introduction of Kree biology has done to Coulson and Garrett has done to them, what about Skye?  My theory still stands that she is already part-Kree, and her lack of reaction to GH325 will be a plot point in the future.

Thankfully, Garrett’s descent didn’t lead to an immediate turnabout from Ward.  Ward did discover just how disposable he was to Garrett, but he was still the good little damaged soldier.  And that’s why it was so easy for May and Skye to lead him into a trap (and a much-deserved beatdown).  I have much love for May, as I love Ming-Na Wen anyway, but it was beyond satisfying to see her put Ward in his place!

Ward’s survival makes it possible to explore his reformation in a lot more detail, should it ever happen.  And why not?  As others have pointed out, The Winter Solider himself did far worse, and yet many were more than willing to accept the possibility of his return to the fold in the end.  So why not Ward?  Frankly, it would have been a waste if they dispensed with him as quickly as the season finale.  A later sacrifice or long redemptive arc would be a lot more satisfying in the end.  Not to mention: how does Simmons deal with Ward in the future, even if Fitz recovers?

Speaking of Fitz, it occurred to me that his medical situation is another big example of what the new status quo for “SHIELD” actually means.  It’s not just a question of weapons or information technology; it’s also access to medical equipment that practically no one else could access.  It also makes me wonder if the surprising “return” of Agent Koenig is a hint that they may be introducing Life Model Decoys in the second season.

With so much to play with in the second season, Coulson’s role as the Director of the new and (hopefully) improved SHIELD is a nice driving force.  It’s not something that has to be a huge part of every episode, yet something that could very well be a linking arc to The Avengers: Age of Ultron.  After all, restoring SHIELD also means dealing with the remnants of Hydra, and as the end of The Winter Soldier demonstrated, there are elements of Hydra that are directly linking into Age of Ultron as well.