On 15th March, 1939, Adolf Hitler ordered the German Army to invade Czechoslovakia. It seemed that war was inevitable. On 8th April, Bolton Wanderers played a home game against Sunderland. Before the game started, Harry Goslin, the team captain, spoke to the crowd: "We are facing a national emergency. But this danger can be met, if everybody keeps a cool head, and knows what to do. This is something you can't leave to the other fellow, everybody has a share to do."
Of the 35 players on the staff of Bolton Wanderers, 32 joined the armed services and the other three went into the coal mines and munitions. This included Harry Hubbick, who resumed his career down the pits and Jack Atkinson and George Hunt served in the local police force. A total of 17 players, including Harry Goslin, Danny Winter, Billy Ithell, Albert Geldard, Tommy Sinclair, Don Howe, Ray Westwood, Ernie Forrest, Jackie Roberts, Jack Hurst and Stan Hanson, joined the 53rd (Bolton) Field Regiment.
The government imposed a fifty mile travelling limit and the Football League divided all the clubs into seven regional areas where games could take place. Bolton Wanderers was put in the North-East League. The team included those players like Harry Hubbick, Jack Atkinson and George Hunt, who had been employed on the home front. Walter Sidebottom, who was later to join the armed forces, emerged as a player with a very bright future. In the 1939-40 season Bolton won 13 out of their 22 games and finished in 4th place in the North-East League.
After being involved in Dunkirk the 53rd (Bolton) Field Regiment spent the rest of 1940 and the whole of 1941 at various army camps around Britain. According to the authors of Wartime Wanderers: They spent their time "building coastal defence constructions, manning anti-aircraft batteries and patrolling potential enemy landing sites all along the East Anglia coastline, variously stationed at Beccles, Nancton and Holt." This enabled them to play the occasional game for Bolton Wanderers in the North-East League. The team that year included Sidebottom, Harry Hubbick, Jack Atkinson, George Hunt, Danny Winter, Billy Ithell, Albert Geldard, Tommy Sinclair, Don Howe, Ray Westwood, Ernie Forrest, Jackie Roberts, Jack Hurst and Stan Hanson.
On 22nd March 1941, George Hunt, the club's leading scorer for the last two seasons, was moved to right-half and replaced at centre-forward by the 15 year-old Nat Lofthouse. Bolton won the game 5-1 with Lofthouse scoring two of the goals. Lofthouse immediately formed a good relationship with Sidebottom and in the first six games together they scored 10 goals between them.
On 26th April 1941, Bolton Wanderers beat Blackburn Rovers 2-0 at Burnden Park. Lofthouse and Sidebottom scored the goals. It was to be Sidebottom's last game for the team as he now fell into the latest age qualification group to be conscripted into the armed forces. Sidebottom was sent to join the Royal Navy.
Walter Sidebottom was drowned when his ship was torpedoed in the English Channel in November 1943.