Produced in parallel with the J2M2 was the J2M3 Raiden (Thunderbolt) Model 21, which was destined to be the major production version. The J2M3 was equipped with a stronger wing carrying four 20-mm cannon. The two fuselage-mounted 7.7 mm machine guns were discarded. Two of the cannon were Model 2 versions with projecting muzzles and the other two were slower-firing Model Is buried entirely inside the wing. The additional wing guns had dictated some local strengthening of the wing structure and required that some reduction be made in the size of the wing-root fuel tanks. The fuselage tank was also slightly reduced in capacity. However, a 44-Imp gall drop tank could be carried underneath the fuselage centerline as an alternative to an external load of a pair of 132-pound bombs underneath the wings. The J2M3 standardized on the enlarged oil cooler with an external air intake that had been introduced during the production run of the J2M2. The Kasei 23a engine was retained.

The J2M3 was initially produced in parallel with the J2M2, but it soon supplanted it and became the major production model of the Raiden. A new domed cockpit canopy (which had been first tried out on the J2M6) was introduced on the production line in June of 1944 in order to address the continual complaints from pilots about poor vision from the cockpit.

The differing type of cannon carried by the J2M3 resulted in different ballistic characteristics. In an attempt to address this problem, the J2M3a Model 21A version was built. The J2M3a differed from the J2M3 only in having the two wing-mounted Type 99 Model 1 20 mm cannon removed and replaced by two 20-mm Type 99 Model 2 cannon carried in pods beneath the wings. The quartet of Model 2 cannon proved more effective, but the drag of the under wing gondolas had an adverse effect on performance, and only 21 of these J2M3a versions were built.

The first J2M3 appeared in October 1943, some time before the J2M2 had been delivered to the 381st Kokutai. This model was adopted in succession to the J2M2 and placed in production at Mitsubishi's Nagoya and Suzuka factories. The first production J2M3 was delivered at the beginning of February 1944.

Unfortunately, the J2M3 was somewhat heavier than the J2M2 owing to its better armament, and the J2M3 could no longer attain the performance called for in the original specification. In addition, its protracted teething troubles and poor mechanical reliability had resulted in slow deliveries and in low availability. Consequently, in June of 1944 the Japanese Navy decided to adopt the Kawanishi N1K1-J Shiden (Allied code name George) as its primary interceptor aircraft. However, production of the Raiden was permitted to continue at a reduced pace until the A7M Reppu (Hurricane) could be placed in production.

However, within weeks of the Japanese Navy's decision to phase out the Raiden, the B-29 Superfortress begin to appear. Since the J2M3 had a good high-altitude performance and an effective armament, it was judged to be a potent B-29 interceptor and its production priority was reinstated. In addition, The Koza Kaigun Kokusho (Koza Naval Air Arsenal) was instructed to join in Raiden production.

The production of Raiden fighters by the Mitsubishi Jugogyo K K of all types totaled 476. The Raiden made its operational debut in September of 1944 over the Marianas during the Battle of the Philippine Sea, when a small number of Raidens had operated from Guam. A technical manual on the Raiden was discovered by American intelligence after the capture of Saipan, and the Raiden was assigned the Allied code name Jack. A small number of Raidens were deployed to the Philippines and were active during the invasion of these islands by the Americans.

The Raiden got its primary use during the defense of the Japanese home islands. Its good performance, powerful armament, and armor protection made it perhaps the best bomber destroyer employed by Japan in the latter stages of the war. It had a good high-altitude performance, and was one of the few Japanese fighters able to reach the high-flying B-29 Superfortress. Its armament of four 20-mm cannon was sufficiently heavy that it could do major damage against B-29s.

In February of 1945, an American technical intelligence team discovered a single Raiden abandoned among the trees alongside the Dewey Boulevard on the outskirts of Manila. It was disassembled and transferred to Clark Field, where it was repaired by the Technical Air Intelligence Command (TAIC) and test flown. A senior test pilot attached to TAIC rated the Raiden as being the best Japanese fighter he had flown, offering a good performance, good stability, good stalling characteristics, and good takeoff and landing qualities. It had a steep climbing angle and a rapid climb rate. Handling and control were good, but the ailerons became rather heavy at speeds above 325 mph. Stalling characteristics were exceptional. Even though there was relatively little stall warning, the recovery from the stall was extremely rapid, with very little altitude being lost. There was no tendency to spin, the aircraft being exceptionally stable. The maneuvering flaps were rated as being very effective. On the negative side, the brakes and rudder brake action were poor, the ailerons were heavy which made the maneuverability fall off at high speeds, the mechanical reliability was poor, and the range was short.

The Raiden was available too late and in insufficient numbers to affect the outcome of the war. It is indeed fortunate for the B-29 crews that more of these capable interceptors were not deployed by the Japanese in the last year of the war.