When the American Civil War broke out some five years later, McWaters joined a group of guerilla fighters, commonly called bushwhackers.
On September 3, 1861, his group sabotaged a bridge that led to the derailment of a Hannibal and St. Joseph Railroad train that carried Union soldiers among its passengers.
He then threw his lot in with Confederate guerilla fighters William T. Anderson and the brothers John and Fletch Taylor in taking out his revenge against Union soldiers and sympathizers.
Later they fell in with Quantrill and crossed over into Kansas where McWaters participated in the Lawrence Massacre in which nearly two hundred men and boys were murdered in retaliation for an 1861 Union raid on Osceola, Missouri.
News accounts of the day reported that during this time McWaters barely escaped Union capture on a number of occasions, often with the assistance of a Jennie Mayfield.
McWaters and Crook later made their escape after wrestling a gun away from a guard during a shift change and with the help of friends fled to the sanctuary of Indian Territory.
[16][17] [18] For a short period McWaters hid among the Niitsítapi People in Nebraska or Wyoming, but this came to an end after he killed a warrior during a dispute over a bottle of whiskey.
[3] During this time detectives hired by Sherriff Farber of Nebraska City had been searching for McWaters and not long after the Weed murder received a tip that he was hiding in Sacramento, California.
The prisoner expressed his perfect willingness to go, intimating that he would not attempt to escape, but the Sheriff, in order to see that he did not, pinioned him hand and foot, and fastened both his leg irons to a ringbolt in the floor of the car.
"[19] On sundry occasions be complained to the officers that something' annoyed him at night and prevented his sleeping, and on Saturday morning be alleged most positively (having evidently been informed of the Mortimer ghost stone?)
that during Friday night something caught hold of his right arm, as he lay on his mattress, and forcing it out upon the floor, sat upon it in such a manner that he could not lift it for a long time.
[3][21] On January 17, 1875, just as he was beginning his long sentence, McWaters instigated a prison uprising that started with the overpowering a guard and the capturing the deputy warden.
Early the next morning a contingent of Company I, 23rd Infantry Regiment (United States) arrived from Omaha and a tense standoff ensued.