There is a really good chance that you had a ton of water that ended up getting blasted sideways into the top of the chimney. It happens, and there is no way to prevent it, nor anything to address once the building dries out. Lots of time and money gets wasted by homeowners and even pros. who fixate on the "fact" that a leak at a chimney is a roof flashing issue. A lot of issues are from water that penetrates the masonry ABOVE the flashing. This could be anything from a one off event like you faced, or degrading masonry, flashing or sealing at the top of the thing. Rebuilding the top 2-4' of an entire chimney to stop leaking is a pretty common situation. My parents had to do a major rebuild of their 70-80 year old, all brick chimney, and the top few feet of the stone and brick one, on our 60 year old place, was rebuilt with a new cap and stainless steel flue caps, a few years back.