They didn't take over...
the CIA was the unit in charge.
Bush. shut. it. down.
Regarding Clinton's chance to get bin Laden:
The 9/11 Commission found
"no credible evidence" that Sudan had ever made such an offer to "hand over bin Laden on a silver platter".
The FBI did not believe we had enough evidence to indict bin Laden at that time, and therefore opposed bringing him to the United States.
Meanwhile, the Clinton administration encouraged Sudan to deport bin Laden back to Saudi Arabia and spent 10 weeks trying to convince the Saudi government to accept him. The Saudis refused.
The Dept. of Justice didn't have an indictment against bin Laden until 1998 – at which point Clinton did order a cruise missile attack on an al Qaeda camp in an attempt to kill bin Laden. Up until then he was seen as a "financier of terrorism" but again, the DOJ did not have the same legal framework to prosecute financiers of terrorism that we have today, thus it would been a charge on paper only, with no backing by any Middle Eastern nation and no sanction power in place yet to put any teeth behind it.