She has delivered the brief to FBI, but no one was going to act on it. But then she could go to the press... so she had to disappear.
The plot of the story is quite thick: oil tycoon Victor Mattiece was planning to drill in the swamplands - the habitat of the endangered pelican species. Knowing that his plan could be jeopardised, he ordered the killing of the Supreme Court Justices who were famous for their pro-environment opinions. At the same time, Mattience has supported the campaign of the President, so even while FBI received the Pelican Brief, they were told to ignore it, because it could endanger the chances for re-elections.
If Debbie would die, Mattiece could proceed with his plan and President would receive his funds for re-election.