As I said in my Coulson/May entry, Coulson’s been the series’ primary protagonist, with Skye as secondary protagonist, but I think that might be about to change, at least for the rest of this season. Which will make more people call her a Mary Sue, except I’m starting to agree with those that think she wouldn’t be getting that fan reaction were she male. At the very least, after a rough start her story’s been very well done, and there’s no reason to think that will change in the upcoming episodes.
Much remains to be determined about that story. Most of what we can speculate on is what we get from googling her birth name(I hold, however that her “real name” remains Skye until she herself decides otherwise, and she doesn’t strike me as likely to, quite frankly). Substitute Coulson for Fury and they’ve kept close to her backstory in a way, but we know from their use of Bobbi Morse that the writers of the MCU are and this series especially not afraid of making bigger changes when convenient. Still, logic would dictate she now needs to learn how to control her powers, and possibly to make use of them the way she does in the comics. From a plotwise standpoint that could be really useful; perhaps the season finale will involve her needing to pull that off. Perhaps saving everyone could even tie into the emotional turmoil the producers have hinted if coming up, as she and those around her try to deal with her connection to Trip’s death and the danger she poses, especially in an underground base where an earthquake could easily leave them all buried. It’s not impossible they may have to keep her somewhere else for at least a while, or she herself might insist on staying somewhere else. Perhaps she may even do an undercover, the way Simmons did. Obviously Hydra are unlikely to buy any defection story, but she might be sent to join her father to keep an eye on him and try to stop him from doing anything too evil. Or she might even be sent to deal with Ward.
But perhaps the more interesting question is the emotional story, how everyone deals with her. I fear the reactions of the likes of Mack, Lance, or Bobbi more, the ones who haven’t spend as much time getting to know her, and aren’t as loyal to Coulson. But even those more loyal to her might struggle. As I said in his entry, I’m sure Coulson would never turn his back on her, but that doesn’t mean he wouldn’t take a lot of lesser measures if he feared for the safety of his base and his people. I wonder if her greatest defender might become May, whose has shown an ability to put her loyalty to a person before her loyalty to S.H.I.E.L.D.. I imagine things might change least between her and her SO, who will be more determined than ever to teach her discipline and skill. And then there’s her reaction to them, whether she starts to push them off, or starts to think they don’t want her.
It might help Skye, at this point in her life, if she could have someone who both loves her and accepts who she is, and does both unconditionally. Plenty of people, heroic and villainous alike, do the former, but the latter is another matter. Coulson and May aren’t in a position to; he has the organization to worry about and it’ll be her job to demand Skye’s improvement. Fitz or especially Simmons might be able to. From a professional standpoint, of course, the old Fitzsimmons would be absolutely fascinated with her to the point of insensitivity, and I suspect Simmons may still try to get her to see the cool side of her new powers, and they might even become much closer over it(much to the happiness of the Skimmons shippers too, of course). Ward by the end of the season also might turn into a candidate, but that situation’s now so complicated I think I’ll leave it to his entry.
And then there’s her father. For the moment, he is completely unable to do the latter. It’s left uncertain if he’s even separated S.H.I.E.L.D. and Hydra enough to not blame the former for her mother’s death, and he clearly is not happy at her choosing the organization and the idea of being a good guy in general over him. But if he, at some point in the future, could accept that? Perhaps some sort of accord could then form between them.
But that would require him not to become the show’s main villain too, and I think he might be headed that way, if only because we don’t have Whitehall anymore, he’s already got that grudge against S.H.I.E.L.D., and it would be easier for him to assume the job than Raina, whose interest in megalomania is much weaker. We don’t know right now if he’s got the ability to transform into Mister Hyde, or if he’s going to get it in the future, but even without it he’s got most of the trappings already. That could possibly end with him dead(they do tend to kill the supervillains off on this show), or possibly just in prison, where his relationship with Skye might still need resolution. Or he might continue on for seasons. Or possibly even show up in the movies. Now that we know he’s one of Marvel’s big villains, he could really go anywhere.