Captain Waddell lowered the Confederate flag , and '' Shenandoah '' underwent physical alteration . Her guns were dismounted and stored below deck , and her hull was painted to look like an ordinary merchant vessel . Regardless of Davis 's proclamation and knowing the unreliability of newspapers at the time , Captain Waddell and his crew knew returning to a U.S. port would mean facing a court sympathetic to the Union . News of President Lincoln 's assassination only served to further diminish any expectation for leniency . The crew predicted that surrendering to federal authorities would run the risk of being tried in a U.S. court and hanged as pirates . Commerce raiders were not included in the reconciliation and amnesty that Confederate soldiers were given . Perhaps more importantly , Waddell would have been aware that the U.S. government no longer had to consider the threat of Confederate retaliation against Union prisoners while determining his crew 's fate . Likely not known to Waddell was that Captain Raphael Semmes of had managed to escape charges of piracy by surrendering on May 1 , 1865 , as an army general under Joseph E. Johnston . Semmes ' former sailors surrendered as artillerymen
President Lincoln 's assassination
Assassination of Abraham Lincoln
CSS Shenandoah