Midnight armed raids, seize documents, arrest for whatever reason you like (blanket pardons cover all crimes y'know), build respective cases.
Perhaps guilt admission is no longer part of pardoning, but pardoning itself implies potential criminal action to be investigated.

Burdick v. United States (1915):

There are substantial differences between legislative immunity and a pardon; the latter carries an imputation of guilt and acceptance of a confession of it, while the former is noncommittal, and tantamount to silence of the witness.

But it was dicta so still debatable if precedent.