On 15 November the ship was assigned to Battleship Division 3 of the 2nd Fleet.
After an aerial attack at Brunei on 16 November, Nagato, Yamato, and the fast battleship Kongō left the following day, bound for Kure.
En route, Kongō and one of the escorting destroyers was sunk by USS Sealion on 21 November.
On 25 November, she arrived at Yokosuka, Japan, for repairs.
Lack of fuel and materials meant that she could not be brought back into service and she was turned into a floating anti-aircraft battery.
Her funnel and mainmast were removed to improve the arcs of fire of her AA guns, which were increased by two Type 89 mounts and nine triple Type 96 gun mounts.
Her forward secondary guns were removed in compensation.
Captain Kiyomi Shibuya relieved Kobe in command of Nagato on 25 November.
Battleship Division 3 was disbanded on 1 January 1945 and the ship was reassigned to Battleship Division 1.
That formation was disbanded on 10 February and she was assigned to the Yokosuka Naval District as a coastal defense ship.
Moored alongside a pier, a coal-burning donkey boiler was installed on the pier for heating and cooking purposes and a converted submarine chaser was positioned alongside to provide steam and electricity; her anti-aircraft guns lacked full power and were only partially operational.
On 20 April, Nagato was reduced to reserve and retired Rear Admiral Miki Otsuka assumed command a week later.

In June 1945, all of her secondary guns and about half of her anti-aircraft armament was moved ashore, together with her rangefinders and searchlights.
Her crew was accordingly reduced to less than 1,000 officers and enlisted men.
On 18 July 1945, the heavily camouflaged ship was attacked by fighter bombers and torpedo bombers from five American carriers as part of Admiral William Halsey Jr.'s campaign to destroy the IJN's last surviving capital ships.
Nagato was hit by two bombs, the first 500-pound (230 kg) bomb struck the bridge and killed Otsuka, the executive officer, and twelve sailors when it detonated upon hitting the roof of the conning tower.
The second 500-pound bomb struck the deck aft of the mainmast and detonated when it hit No.
3 barbette.
It failed to damage the barbette or the turret above it, but blew a hole nearly 12 feet (3.7 m) in diameter in the deck above the officer's lounge, killing 21 men and damaging four Type 96 guns on the deck above.
A dud rocket of uncertain size hit the ship's fantail, but failed to do any significant damage.
To convince the Americans that Nagato had been badly damaged by the attack, her damage was left unrepaired and some of her ballast tanks were pumped full of seawater to make her sit deeper in the water as if she had sunk to the harbor bottom.

Captain Shuichi Sugino was appointed as Nagato's new captain on 24 July, but he was unable to take up his appointment until 20 August.
Retired Rear Admiral Masamichi Ikeguchi was assigned as the ship's interim captain until Sugino arrived.
The Yokosuka Naval District received an alarm on the night of 1/2 August that a large convoy was approaching Sagami Bay and Nagato was ordered to attack immediately.
The ship was totally unprepared for any attack, but Ikeguchi began the necessary preparations.
The water in the ballast compartments was pumped out and her crew began reloading the propellant charges for her 16-inch guns.
The ship received more fuel from a barge later that morning, but no order to attack ever came as it had been a false alarm.
Sailors from the battleship USS Iowa, Underwater Demolition Team 18, and the high-speed transport USS Horace A. Bass secured the battleship on 30 August after the occupation began and Captain Thomas J  Flynn, executive officer of the Iowa, assumed command.
By the time the war ended, Nagato was the only Japanese battleship still afloat.
She was stricken from the Navy List on 15 September.
On 15 November the ship was assigned to Battleship Division 3 of the 2nd Fleet. After an aerial attack at Brunei on 16 November, Nagato, Yamato, and the fast battleship Kongō left the following day, bound for Kure. En route, Kongō and one of the escorting destroyers was sunk by USS Sealion on 21 November. On 25 November, she arrived at Yokosuka, Japan, for repairs. Lack of fuel and materials meant that she could not be brought back into service and she was turned into a floating anti-aircraft battery. Her funnel and mainmast were removed to improve the arcs of fire of her AA guns, which were increased by two Type 89 mounts and nine triple Type 96 gun mounts. Her forward secondary guns were removed in compensation. Captain Kiyomi Shibuya relieved Kobe in command of Nagato on 25 November. Battleship Division 3 was disbanded on 1 January 1945 and the ship was reassigned to Battleship Division 1. That formation was disbanded on 10 February and she was assigned to the Yokosuka Naval District as a coastal defense ship. Moored alongside a pier, a coal-burning donkey boiler was installed on the pier for heating and cooking purposes and a converted submarine chaser was positioned alongside to provide steam and electricity; her anti-aircraft guns lacked full power and were only partially operational. On 20 April, Nagato was reduced to reserve and retired Rear Admiral Miki Otsuka assumed command a week later.
In June 1945, all of her secondary guns and about half of her anti-aircraft armament was moved ashore, together with her rangefinders and searchlights. Her crew was accordingly reduced to less than 1,000 officers and enlisted men. On 18 July 1945, the heavily camouflaged ship was attacked by fighter bombers and torpedo bombers from five American carriers as part of Admiral William Halsey Jr.'s campaign to destroy the IJN's last surviving capital ships. Nagato was hit by two bombs, the first 500-pound (230 kg) bomb struck the bridge and killed Otsuka, the executive officer, and twelve sailors when it detonated upon hitting the roof of the conning tower. The second 500-pound bomb struck the deck aft of the mainmast and detonated when it hit No. 3 barbette. It failed to damage the barbette or the turret above it, but blew a hole nearly 12 feet (3.7 m) in diameter in the deck above the officer's lounge, killing 21 men and damaging four Type 96 guns on the deck above. A dud rocket of uncertain size hit the ship's fantail, but failed to do any significant damage. To convince the Americans that Nagato had been badly damaged by the attack, her damage was left unrepaired and some of her ballast tanks were pumped full of seawater to make her sit deeper in the water as if she had sunk to the harbor bottom.
Captain Shuichi Sugino was appointed as Nagato's new captain on 24 July, but he was unable to take up his appointment until 20 August. Retired Rear Admiral Masamichi Ikeguchi was assigned as the ship's interim captain until Sugino arrived. The Yokosuka Naval District received an alarm on the night of 1/2 August that a large convoy was approaching Sagami Bay and Nagato was ordered to attack immediately. The ship was totally unprepared for any attack, but Ikeguchi began the necessary preparations. The water in the ballast compartments was pumped out and her crew began reloading the propellant charges for her 16-inch guns. The ship received more fuel from a barge later that morning, but no order to attack ever came as it had been a false alarm. Sailors from the battleship USS Iowa, Underwater Demolition Team 18, and the high-speed transport USS Horace A. Bass secured the battleship on 30 August after the occupation began and Captain Thomas J  Flynn, executive officer of the Iowa, assumed command. By the time the war ended, Nagato was the only Japanese battleship still afloat. She was stricken from the Navy List on 15 September.
Japanese battleship Nagato