From December 1939 numerous army personnel were stationed around Raymond Terrace for training and other war purposes. The Commonwealth government purchased land near Williamtown in early 1940 and established a Royal Australian Air Force (RAAF) base to defend the northern approaches to Newcastle and Sydney at a time of increasing threat by enemy aggression. From 1941 the new Williamtown RAAF Base brought more servicemen and construction workers into the area. Some local women remember those as the years they could go to dances in various halls six nights a week! They enjoyed a hectic social life unexpected by small town residents.

1942 was a worrying year for Australia as Darwin was bombed and a number of coastal cities were shelled, including nearby Newcastle. Fort Tomaree was constructed to protect Port Stephens. The main defensive weapons were two six inch (152mm) guns, capable of penetrating 150mm of steel at 14 kilometres. Their purpose was to sink shipping. The stated aim of Fort Tomaree was "to deny the use of the Port to an attacking force". Troops were housed in buildings now taken over by Tomaree Lodge. Most of the relics that were part of Fort Tomaree lie in Tomaree National Park.

The guns were never fired in anger and the massive concrete structures that housed the guns are accessible by a walking track from the car park at Zenith Beach.

At the water's edge a jetty was built to hold two torpedo tubes, a last defence against enemy shipping. Two other gun emplacements housed three pounder guns known as the 'surf battery', to provide defence against fast moving vessels. For over half a century these reinforced concrete structures have survived the wear of salt spray and curious visitors. They stand a silent seaward watch, their job completed.

Fort Tomaree also had anti-aircraft guns, searchlights, observation posts and plotting rooms. An Air Force early warning radar was located at the top of the Tomaree hill.

“Sometime during July, [1942] around 1530 hours we spotted a periscope travelling northwards so it was promptly reported to Fighter Sector. Time went by, we followed its straight line path for about an hour. Nothing happened until about 1800 hours when a Walrus appeared to survey the scene, of course by then the submarine had long since departed leaving us to wonder about the activities of Fighter Sector."

– Excerpts from "The Guns of Tomaree" by Michael Smith and Graeme Steinbeck.

Approval was granted by the Australian War Cabinet to establish “HMAS Assault”, an RAN Naval Training Centre, in the Port Stephens area of New South Wales. The site was chosen after an aerial inspection in June 1942 because it was a safe haven from the Japanese Submarine activity occurring off the east coast of Australia and because the locality was mostly a small isolated fishing village.

HMAS Westralia arrived on 3 September 1942 to provide interim accommodation until "HMAS Assault" was completed.
The Allied Works Council erected numerous buildings including the Sick Bay, which now houses the Port Stephens Community Arts Centre at Nelson Bay. The Naval Training Centre at "HMAS Assault" was used to train landing craft crews, beach parties and signal teams.

General Macarthur recognised in 1942 the need to train troops and ships' companies engaged in combined operations against the Japanese in the South West Pacific. Port Stephens was chosen for this facility known as the Joint Overseas Operating Training School (JOOTS). On 1 March 1943, the Joint Operational Overseas Training School, HMAS Assault and U.S. Advanced Base Unit were all combined to form the Amphibious Training Command. 2000 Australian and 20,000 U.S. servicemen trained for beach landings in 1943-¬44. To enable the construction of the many huts and other facilities required, the crude tracks through the sandhills and swamps were re-routed or rebuilt to negotiable road standard. Town water and electricity were brought to the area providing infrastructure beneficial for the few residents and the development of a more permanent settlement. The facilities constructed in 1943 with the improved access and services laid the foundations for the post-war growth the area enjoyed.

Amongst large ships anchored in the Port during that time were two Australian coastal liners converted to troop transports, the HMAS Manoora and HMAS Westralia (which later saw involvement in many beach attacks) and the USS Henry T. Allen. These ships were involved in landings under simulated invasion conditions on Zenith Beach, Wreck Beach and Box Beach in readiness for the amphibious invasions of Dutch New Guinea, Tarakan, Balikpan, as well as the Leyte and Lingayan invasions in the Philippines.

In October 1943, there were 141 ships and landing craft (including thirteen Australian built) based at Port Stephens. 36 of these ships were controlled by HMAS Assault and 105 by the US Navy.

An Army camp was also established at Gan Gan, 4km from Nelson Bay, it was a troop staging and training area. The buildings there consisted of kitchens, mess, toilets and ablution blocks with the personnel living in tents.

Read about the post War development of Port Stephens - click here.