As the gunsmoke began to clear on Ruby Ridge, prosecution of the Weaver case was assigned to U.S. Attorney Ron Howen.  Randy Weaver and Kevin Harris were commended to the Ada County Jail and eventually charged with ten counts, including murder, aiding and abetting murder, conspiracy and assault.  With the wealth of information to sift through, the trial would not begin for another eight months, during which time Kevin and Randy remained incarcerated.

On April 13, 1993, a jury consisting of seven women and five men, along with six alternates was selected at the Federal Courthouse in Boise, Idaho, with U.S. District Court Judge Edward J. Lodge presiding.  The trial began the following day and ultimately lasted for a total of 36 days.  During the trial, the prosecution called 56 witnesses, while the defense, confident that the government would destroy their own case, called none.  The entire ordeal was bizarre to say the least and almost everyone of the prosecution’s witnesses contradicted or countered the testimony of a previous witness.  The prosecution spent several days going over the Weavers' religious views, trying to establish that they were racist and had a long-lived conspiracy to violently confront the government.  Marshall service witnesses described pre-siege scenarios to root Weaver out of his cabin, however when pressed by the defense, they said they never considered simply knocking on the door and arresting him.  In addition, government agents admitted that the FBI had tampered with evidence and that the crime scene photos given to the defense were phony reenactments.  Even though the prosecutor knew this, he had failed to inform the defense and it was only during the trial that these facts came to light.  For prosecutorial misconduct, the judge ordered the government to pay part of the defense attorneys' fees ─ an action almost unheard of in a criminal case.  Prosecutor Ron Howen was also was forced to apologize in open court. 

The defense countered the prosecution’s conspiracy arguments by stating that the Weaver family had moved to northern Idaho in 1983 to practice their religion in peace.  They wanted to be left alone.  It was then alleged that Randy had been set up on the weapons’ charge and that federal agents sought to arrest him when he refused to become an informant.  The resulting failure- to-appear charges were then brought because Randy Weaver was given an incorrect court date and then indicted before that date.  The defense continued by arguing that the shootout was a direct result of federal agent Arthur Roderick’s actions, in which he killed the Weaver family dog in proximity to Samuel Weaver, which caused Samuel to return fire in self-defense.  Finally, the defense claimed that Vicki Weaver was murdered in cold blood by FBI sniper Lon Horiuchi.