I'm gonna go with the Goodell assassins vs. Belichick/Jones/Gronk story. It seems like the most logical story supported by the most evidence. Here's how I think it went down:
1. First wave of assassins easily dispatched by the boys, though Bill did take one in the eye because, let's face it, he is getting a bit old for this s***.
2. Second wave gives up quickly and flees. Bill enacts the Golden Goose Protocol and orders Ernie Adams to get his black ops team to the Brady/Bundchen residence ASAP to be safe.
3. Jones heads to the local police and informs them of the attempted assault and resulting beatdown. Authorities refer him to the hospital for a minor katana-based injury and head to his house to "secure the residence." (i.e. check out the crime scene)
4. Gronk lets no man get away from him; he hunts the assassins down and ultimately catches them in central New York calling Mike Kensil from a payphone giving him the "bad news" to give to Roger. He disposes of them quickly, but it takes him a little while to get back to MA so he misses practice.
I'm pretty sure this is what happened.