I feel like this scene often gets overlooked among the many other “moments where Leo Fitz is so clearly in love with Jemma Simmons that it offends me.” In his mind for these few seconds, Fitz has failed to protect Jemma - whatever the mystery grenade was went off, and for all he knows he’s just watched her die in front of him without being able to stop it. Skye sees this and automatically runs over to assess Jemma’s health, but Fitz’s reaction is very different and interesting. In the previous 12 episodes of season 1 he’s been shown to be fairly proactive in catastrophic situations, including in FZZT when he watches her jump out of the plane. In that situation, he sees what might be to others an insurmountable problem (her falling out of a plane 30,000 feet in the air) and goes straight for the parachute - there’s no way he’s letting her go that easily.
In TRACKS, however, he freezes - the probably deadly weapon has already gone off and he doesn’t think he has any recourse to fix it (without her medical assistance & biochemical expertise). Rather than behave as he normally might (by working to find a solution), Fitz can barely move. It’s as if all his muscles have spontaneously atrophied, as if the slower he moves the longer he has before he learns that Jemma really is dead. It isn’t just his legs either - even his arms move jerkily. Thanks to Skye keeping her head about her, it isn’t more than a few seconds before Fitz learns that Jemma’s just unconscious and not dead. But his complete and utter paralysis in the face of having possibly watched Jemma die is I think very indicative of how his feelings for her have progressed since the last time he saw her in immediate danger. This time, he stops functioning almost instantly, and you can practically hear him thinking “no, no, no, no” as he stares at Jemma’s body. He almost collapses when he learns that she’s alive and he bends in half, leaning on a box and needing support as he forces himself to let go of that complete and utter horror.
Later in the episode, we see Fitz comforting Jemma after she fights so desperately to save Skye’s life, but I think to some degree in that scene he’s comforting himself as well. He thought he watched her try to sacrifice herself for a second time earlier that day, and that particular fear isn’t something that’s easy for him to forget.