It is practically impossible to know what will happen to the Muslim Brotherhood now. It is very difficult to predict how things like this will turn out while we are still in the middle of those events.
If I had to bet money, I would project that the Brotherhood will have a status somewhere in between that which they held under the rule of Hosni Mubarak and that which they held when they were in power before the coup that overthrew Morsi. The Brotherhood will almost surely not be allowed back into power in the near future. The military clearly does not trust the Brotherhood and it clearly has too much power for the Brotherhood to overcome at this point. The military seems determined, as can be seen from the recent shootings, to keep the Islamists out of power.
On the other hand, it seems unlikely that the military will go so far as to outlaw the Brotherhood as was previously done. I would argue that there would be too much pressure from both within Egypt and from the outside world. There has been movement towards democracy in Egypt and domestic and foreign forces want that to continue. Full-on suppression of the Brotherhood therefore seems unlikely.
I would imagine, then, that the Brotherhood will remain legal, but that it will function as something of an opposition force in Egyptian politics.