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how do you prevent the corruption of the new entity?

By decentralizing it.

The solution to this is to dismantle the FBI as we know it today and replace it with a decentralized investigative body organized by the states.
I'm reposting my idea from March 5, 2018 (reformatted for easier reading):
As I was reading this article (As D.C. Corruption Mounts, Heres How The American People Can Get Justice), I was beginning to think of a solution that was close to where the author ended up.
What if the FBI were disbanded as a federal agency, and replaced by a different organization that was populated by the states themselves?
Each state would delegate a number of investigators to serve at the pleasure of their home state, and this body would become a decentralized federal investigative bureau, managed by the states.
As is with the militia, the Constitution provides for calling up the militias for national service, but the officers are selected by the states.
It isn't a stretch to declare that state militias have investigators as a component of a military police, perhaps made up of local police department detectives who are also in the state national guard reserves.
Use the militia clause in the Constitution to call up the state militias' investigative arms for federal service, with state appointed officers.
Each state can create a branch of their militia as MPs, or detectives. These people would report to militia officers appointed within each state, and then these militia branches (officers and detectives) would be called up at the request the Commander-In-Chief and approval by Congress (Article I Section 8: "to provide for calling forth the Militia to execute the Laws of the Union, suppress Insurrections and repel Invasions,") to serve a national priority such as investigating a particular federal crime, under the authority of state officers, not federal bureaucrats.
The state officers will report directly to the Commander-In-Chief (Article II Section II: "The President shall be Commander in Chief of the Army and Navy of the United States, and of the Militia of the several States, when called into the actual Service of the United States").
Once the investigation is complete, the investigating team is released back to the states.
If a crime occurred in one state, then the militia police from another state can be called up to investigate.
Several investigations across several states can operate in parallel, if needed.
Root cause analyses looks for systemic causes of failures, not behavioral causes.
Part of that review is identifying the protective systems that were in place to prevent what happened from happening, and to brainstorm additional protective systems to catch whatever still slipped through.
Management enforcement of process compliance with consequences for failure to comply is a protective system.
Lax management enforcement of process compliance might be a systemic cause if the fix were to reinforce the importance of process compliance and put consequences on management for lack of process discipline.
However, in the recent examples of FBI failure, management was not lax in oversight, they were also complicit actors in avoiding the process. This is still behavioral, so the systemic root cause is not yet found.
I'm going to suggest that the systemic root cause of the recent FBI disfunction is the "independent" nature of the FBI itself.
This was magnified by the behavioral causes that top management felt they were unaccountable to anyone;
that a single ideological mindset became established through years of political appointments that controlled the hiring practices of lower-level staff;
that using management reinforcement to correct the root cause was ineffective given that management was a part of the problem, if not leading the effort.
Therefore, we must look to other protective systems for corrections.
One protective system is the Inspector General. While this seems to be working now, in hindsight it doesn't seem to have been effective at the time the actions were taking place.
When the bad actors are the top management itself in a department, an IG is too easily bypassed. Therefore, a new protective system must be put in place.
My proposed corrective system is to replace a federal-centric FBI with a state-centric investigative agency.
This agency would have distributed leadership, since by following the militia model in the Constitution, the "officers" would be selected by the states and would be subject to recall at the whim of the home state.
A single monolithic mindset cannot become entrenched, since concerned states can replace their officers at any time.
I suggested attaching this investigative militia to the Commander-In-Chief directly on a case-by-case basis, with some provision for a senior officer hierarchy to manage separate state contingents.
Since Congress has the authority to call up the militia, but the President is the Commander-In-Chief of the militia, there is a check-and-balance already in place.
If a state investigative team finds evidence of a crime, the President can refer charges to the Department of Justice for further prosecutorial action.
There would be no need for a Special Prosecutor, as the investigative arm of the called up militia units can do this.
The Department of Justice can aid the investigations with grand juries, and criminal referrals would be passed along to the Department of Justice for action.
The President can then release the militia units back to the states, preventing a runaway special prosecutor from expanding the scope of the investigation.
"Process crimes," such as lying to the FBI, would go away as an especially nefarious tool of an over-zealous prosecutor.
A decentralized national investigative structure, overseen by the states but controlled by the commander-in-chief on a case-by-case basis, may be the best way to restore confidence that such an agency is not corrupted by national party bloc interests.

The idea is that investigators in one state would be called up to investigate a crime committed in another state. This can be done now without any constitutional amendments with my plan. This state decentralization would stop the politicization of using the FBI as a weapon of the Democrats.

-PJ