General Abdel Fattah el-Sisi, was originally Morsi's man. Morsi appointed him to the top spot because of Sisi's friendliness to the Muslim Brotherhood.
On the surface this is a fairly simple standoff between Morsi, the Brotherhood's President of Egypt, the liberal protesters and the military which has decided to
1. Throw in with the protesters
2. Force stability on Egypt the hard way by setting up some kind of unity government
3. Take over the country
Any number of these options are a possibility.
But politics in the region is a messy business. The motive of the liberals in taking down Morsi is obvious. Morsi built up a powerful clique and used that to leverage total control over Egypt. Even if he hadn't done that, this probably would have happened because there are too many newly minted professional revolutionaries and too many liberal leaders convinced that they will do better next time around.
The motives on the military side are less clear.
The Egyptian military, like most of the region's militaries, does have a history of taking over the government. Mubarak, Sadat and Nasser were all members of the military.
But General Abdel Fattah el-Sisi, aside from having a silly sounding name, was originally Morsi's man. Morsi appointed him to the top spot, skipping him ahead of better qualified officers because of Sisi's reported friendliness to the Muslim Brotherhood.
Sisi, a career soldier, was head of military intelligence and the youngest member of the 19-strong Supreme Council of the Armed Forces. But despite coming from the heart of the security establishment he had a reputation for being sympathetic to the Muslim Brotherhood — the reason, many Egyptians assumed, Morsi chose him for the job. Sisi is said to be a religious man, and his wife, unusually, wears the full niqab.
Eyebrows were raised when Sisi decided to allow Islamists to enter the Egyptian military's officer training academy — when it had always insisted before that cadets were unimpeachably apolitical.
It wouldn't be unprecedented for Sisi, despite all this, to stab Morsi in the back. And if Sisi really is as uncomfortable with the job as some reports claim, he may simply be taking orders from the military men who should have had his job.
Unless the Muslim Brotherhood is really playing both sides.
Morsi did not enjoy universal support within the Brotherhood and while he has gotten the organization pretty far along the road, it may have a fallback plan for his overthrow.
Injecting the military into the process and allowing it to influence the post-Morsi government, under a friendly general, might be its fallback plan.
That's all speculation of course. The Brotherhood has yet to make any significantly conciliatory gestures. It has given every appearance of being willing to fight for Morsi until the end. But it's also too wily not to have a Plan B.