You guys know I love to analyze body language (as demonstrated in a couple metas here, here, and here) and the differences between episode 1 and episode 3 show a lot of progress for the Skyeward ship, so let’s discuss exactly we’re seeing here.
Look at the the first two scenes. In 2x01, we see both of them looking incredibly tense and uncomfortable. Ward is standing straight and stiff, while Skye is sitting up straight in her chair - they’re both acting very formal around each other. Serious. Official. Skye specifically is sitting on the edge of her seat. She’s ready to bolt if needed, she’s already got an exit strategy in place. She very clearly does not want to be there. But look at the huge difference in 2x03. Ward is leaning against the wall, casually, comfortably. Skye is seated all the way back in her chair, her arms on the armrests. She may not necessarily be happy to be there, but she’s also no longer looking to leave as soon as she can. They’re much more comfortable in each other’s presence now and we can see very clearly that they are slowly starting to rebuild their relationship. It’s interesting to note that Ward never sits on the bed when he’s talking to her. Because sitting down would place him farther away from her physically. So in the first scene, he’s standing because he wants to be as close to her as he can without making the already tense atmosphere even more uncomfortable for her. In the second scene, he still wants to be physically close to her, so he leans against the wall because the atmosphere between them has become slightly more casual and comfortable.
The next two scenes show us how Skye talks to him. In 2x01, she’s acting purely as an agent, there to gather intel. She’s wearing all black and her movements are even slightly robotic, from the way she kind of tilts her head to the way she speaks to him very formally. In 2x03, on the other hand, we see a bit of her personality - she’s sarcastic and a bit more animated. It’s also noteworthy that she’s wearing a blue shirt, she’s wearing a color! She may be coming to Ward for intel, but she’s also coming to him as more than an agent this time, she’s coming to him as one human being to another, instead of as an agent to a prisoner.
The last two scenes show us how she reacts to Ward trying to get personal. In 2x01, she immediately gets up and starts to walk out. She immediately shuts him out, refusing to listen to what he has to say. She is setting an example, showing him that she’s in control, that she doesn’t have time for chitchat, that she’s only here on official SHIELD business. She doesn’t want to get personal with him, not again. But in 2x03, while she again interrupts him and doesn’t let him finish, she actually stays in her seat this time. She still shows that she’s in charge by directing the conversation towards the topic she wants to discuss, but she doesn’t threaten to leave this time, which shows that she’s more comfortable around him, and no longer quite so eager to get away from him.
Look at how far we’ve come between these two interrogation scenes. In the first one, they’re both tense and formal, and Skye especially acts robotic, focused on her mission. But in the second set, we see how they’re once again opening up to each other, how their relationship is starting back up again. And in both scenes, their poses mimic each other - both Ward and Skye are tense in 2x01 and both Skye and Ward are more casual in 2x03. Whether consciously or not, even their body language is in sync.
The ship is nowhere near over. It’s just beginning.