In October 1942, he was assigned as aide to the commander of the Naval Air Station Ottumwa in Iowa until May 1943.  On October 1, 1943, Nixon was promoted to lieutenant .  Seeking more excitement, he requested sea duty and was reassigned as the naval passenger control officer for the South Pacific Combat Air Transport Command , supporting the logistics of operations in the South West Pacific theater ;   he was the Officer in Charge of the Combat Air Transport Command at Guadalcanal in the Solomons and in March 1944 at Green Island ( Nissan Island ) just north of Bougainville .  His unit prepared manifests and flight plans for C-47 operations and supervised the loading and unloading of the cargo aircraft. For this service, he received a Navy Letter of Commendation (awarded a Navy Commendation Ribbon which was later updated to the Navy and Marine Corps Commendation Medal ) from his commanding officer for "meritorious and efficient performance of duty as Officer in Charge of the South Pacific Combat Air Transport Command". Upon his return to the ., Nixon was appointed the administrative officer of the Alameda Naval Air Station in California. In January 1945, he was transferred to the Bureau of Aeronautics office in Philadelphia to help negotiate the termination of war contracts, and received his second letter of commendation, from the Secretary of the Navy  for "meritorious service, tireless effort, and devotion to duty". Later, Nixon was transferred to other offices to work on contracts and finally to Baltimore.  On October 3, 1945, he was promoted to lieutenant commander .   On March 10, 1946, he was relieved of active duty.  He resigned his commission on New Year's Day 1946.  On June 1, 1953, he was promoted to commander.  He retired in the . Naval Reserve on June 6, 1966. 
On June 19, 1972, the press reported that one of the Watergate burglars was a Republican Party security aide.  Former Attorney General John Mitchell, who at the time was the head of the CRP, denied any involvement with the Watergate break-in or knowledge of the five burglars.   On August 1, a $25,000 cashier’s check earmarked for the Nixon re-election campaign was found in the bank account of one of the Watergate burglars. Further investigation by the FBI would reveal the team had thousands of dollars more to support their travel and expenses in the months leading up to their arrests. Examination of their funds showed a link to the finance committee of the CRP.
On Oct. 10, 1972, we wrote a story in The Post outlining the extensive sabotage and spying operations of the Nixon campaign and White House, particularly against Muskie, and stating that the Watergate burglary was not an isolated event. The story said that at least 50 operatives had been involved in the espionage and sabotage, many of them under the direction of a young California lawyer named Donald Segretti; several days later, we reported that Segretti had been hired by Dwight Chapin, Nixon’s appointments secretary. (The Senate Watergate committee later found more than 50 saboteurs, including 22 who were paid by Segretti.) Herbert Kalmbach, Nixon’s personal attorney, paid Segretti more than $43,000 from leftover campaign funds for these activities. Throughout the operation, Segretti was contacted regularly by Howard Hunt.