Nice theory, but the senior agent who called in an 0-84 was killed by a bullet. Cal wouldn't kill him with a bullet. Hydra might if he wasn't one of them, but in that case, Skye was apparently actually classified an 0-84 (so that SHIELD agents who weren't HYDRA agents would also go after her).
An alternative would be that Cal didn't do all of the killings on his own, and Jiaying did some too, with a gun. That would be compatible with the rest of your theory.
Actually, now I'm getting confused. Didn't Cal say he didn't begin his... experimentation... until
after Skye and Jiaying had been taken from him? If so, I see no reason to think he wouldn't have used a gun. Granted, this also makes the whole talk of "monsters" at Hunan to be a bit of hyperbole. Do I smell a retcon? Hopefully we get answers when we see what happens with Hyde next week.
At any rate, my version of events is similar to Usok's:
- A HYDRA leader in SHIELD (Pierce?) orders a team to search for Jiaying (the exact composition of this team, in terms of HYDRA vs. SHIELD is somewhat irrelevant, as they're just following orders, protecting the world from enhanced).
- The team discovers the baby instead, tries to take her as well.
- A fight with Cal & Jiangying ensues.
- One detachment of HYDRA agents manage to capture Jianying, and takes her to Whitehall's base. Pierce releases Whitehall to continue his experimentation there.
- The remaining HYDRA/SHIELD agents are slaughtered, but one manages to hide under a bridge with the baby before dying. How much of this slaughter is internal SHIELD/HYDRA fighting vs. Cal (or other Inhumans???) fighting them is unknown.
- The SHIELD rookies running back-end move in and see the destruction. They have no idea of HYDRA or of Cal and Jiangying. They find the baby in the dead operatives arms, assume she's the 0-8-4, and take her for her own safety.
- What isn't clear to me is the intentions of the dead senior operative: was he HYDRA, kidnapping Skye, or a SHIELD loyalist, trying to protect her? I suspect the former.
- Do we know if it was HYDRA or Cal who starts tracking down and killing the rookie SHIELD agents?