During the protracted war, the Senate handed over to Palpatine the power of the Assembly to bring an early end to the war. Since a corrupt democracy could not pass resolutions quickly enough in emergencies, Palpatine's powers were strengthened to save debate and enable him to take immediate action. The Senate was relieved because Palpatine had promised to return many of the powers borrowed from the Assembly once the crisis situation had died down. The archaic constitution that had not changed over the years would be radically rewritten (as a temporary fix) as an "efficient, living constitution. Disappointed with the corrupt republican government of a corrupt parliament and bureaucracy, the people would come to strongly support a consolidated, centralized society with Palpatine and military commissions that would be rapidly developed by the war. There was security to ensure safety from CIS attacks or internal treason during the war. Palpatine was also active in this, with an oath to guarantee the security and stability of his beloved Republic until the war was won.
The Jedi Council continued to protect Palpatine with excessive vigilance. However, they began to feel uncomfortable that Palpatine was legitimately taking over many of the functions that the Senate should have. For many years, the Jedi felt that serving the Republic was about respecting the resolutions of the Assembly.
The unexpected incident of Palpatine's kidnapping occurs. If Palpatine dies, the Republic, which has become a police state, will easily collapse. In the end, Palpatine survives, but due to the weakness of security, he makes a motion to have Palpatine oversee the Jedi Council, which is responsible for military operations. He thought that this would speed up military operations and make a big step towards victory. This would mean that the Chancellor would have the authority to oversee and direct the Jedi Council without the interference of the Senate.
The Council is furious that the Senate has effectively ceased to interfere.
And the Council decides that when the crisis dissipates, the Council will either give up its authority to the Chancellor or, if the Chancellor refuses, the Council will be forced to take over.
Sensing this, Palpatine explains to Skywalker
"In the wake of the kidnapping, I became commander in chief of the army. I want to end the war quickly and return all authority to the Senate, where it belongs, in order to disarm it. But what I fear most is that the Jedi Council will take over the position of Supreme Commander! If that happens, the council will have the army under its supervision after the war without the interference of the senate!
