During 1943, when the war in the air reached a new peak of ferocity, the Luftwaffe was holding its own at least in German skies, and aircraft production was reaching new levels. The air war was, however, very much one of attrition, so there was official reluctance to countenance the loss of production associated with bringing new types of aircraft into service, despite the fact that the Luftwaffe was losing ground in the performance of its aircraft. Thus, the practice of modifying and improving aircraft currently in production was much in favor, and the RLM enthusiastically selected aircraft for development from a range of Junkers' proposals based on the Ju 188. There was an urgent need to improve both speed and altitude of all classes of aircraft, and this led to development of the Ju 188 S and Ju 188 T high-altitude intruder and reconnaissance aircraft.
Also selected for parallel development with these two types were the Ju 188 J night and bad-weather fighter, the Ju 188 K bomber and the Ju 188 L reconnaissance aircraft, all three being designed for high-altitude operation and, as far as possible, to have common airframes with equipment differing only to suit their different roles. These three types were considered especially important and were therefore redesignated Ju 388 J, Ju 388 K, and Ju 388 L in September 1943 for development in a program code-named Hubertus. The Ju 388 K and Ju 388 L were similar to the Ju 188 S and Ju 188 T, and had similar pressurized nose sections, but for the Ju 388 J a new design of pressurized cabin was necessary because of the nose-mounted radar equipment. One of the new features planned for all Ju 388s was the fitting of a remote-controlled FA 15 tail barbette mounting two 0.511 in (13 mm) MG 131 machine guns, this being the sole armament in the case of the Ju 388 K and Ju 388 L.
It was planned to use for all three models the Junkers Jumo 213E-1 engines (as for the Ju 188 S and Ju 188 T), but, because of a doubtful supply situation, the 1,800 hp BMW 801TJ air-cooled radial engine with turbo-supercharger was selected instead.
Late in 1943, the Ju 388 V1 was built from a Ju 188 T air frame as the prototype for the Ju 388 L reconnaissance machine, and this was followed in January 1944 by the Ju 388 V3 as the prototype for the Ju 388 K bomber. Later still, the Ju 388 V2 was the prototype for the Ju 388 J Störtebeker (named after a 15th-century German pirate) fighter. Successful trials with these prototypes led to plans for production despite difficulties in the development of the remote-controlled armament being tested in a Ju 188 C-0. The Jägerstab, which radically revised the production programs for aircraft, had its Program 226 accepted on July 8, 1944, and called for a monthly output of between 300 and 400 of the Ju 388s compared with only 180 of the Ju 88 night-fighters and 50 Heinkel He 219s per month. These figures reflect considerable faith in the Ju 388 and, although by then Hitler was being persuaded to abandon conventional bombers, the Ju 388 K bomber still went ahead.
By July 1944, the first of ten Ju 388 K-0 pre-production bombers were leaving the Dessau plant, although no tail barbettes were available for them. Only five production Ju 388 K-1s were built before production had to stop early in 1945, but these aircraft did receive the FA 15 tail barbette. The bomb load for this type was carried beneath the fuselage but was enclosed by a large wooden ventral fairing. Although up to 6,610 lb (3,000 kg) of bombs could be carried, a more conventional load was about 4,410 lb (2,000 kg) of bombs, e.g. one SC 1800 Satan or two SC 1000 Hermann bombs. Further planned versions of the Ju 388 K were the Ju 388 K-2 with Junkers Jumo 213E-1 engines and the Ju 388 K-3 with Junkers Jumo 222E engines.
Responsibility for the Ju 388 L reconnaissance aircraft was given to the Allgemeine Transportanlagen GmbH (ATG) at Merseburg near Leipzig where the first ten pre-production Ju 388 L-0s were built from Ju 188 S-1 airframes. By August 1944, the first of these were being dispatched to Erprobungskommando 388 for Service evaluation and, by October, the first production Ju 388 L-1s were being completed.
Once again, the FA 15 barbette was not available for the pre-production machines, which were fitted with fixed twin 0.311 in (7.9 mm) MG 81 machine guns firing aft from a ventral housing. Although the FA 15 barbette was fitted to the production Ju 388 L-1s, it was still under-developed and was therefore later supplemented by another 0.511 in (13 mm) MG 131 in the rear of the cabin glazing. An extra, fourth crew member was needed to operate this gun, and the modified aircraft was redesignated Ju 388 L-1/b. The Ju 388 L-1 had a large wooden ventral fairing (similar to the Ju 388 K) in which were carried two day or night cameras of the same type used with the Ju 188F. A jettisonable auxiliary fuel tank could also be carried in the fairing to give a total maximum fuel capacity of 1,276 gal (4,830 l), and FuG 217 Neptun tail-mounted warning radar was fitted.
A few Ju 388 L-3s were built that differed in having Junkers Jumo 213E-1 engines with MW-50 boosting. Before Ju 388 L production stopped in December 1944, the Weser-Flugzeugbau joined in with ATG but only produced ten examples. Although the Ju 388 L was issued to the Luftwaffe, it never became fully operational with the conventional long-range reconnaissance units. The special Versuchsverband Ob.d.L. operated three Ju 388 Ls, one being coded T9-DL.
While the Ju 388 J Störtebeker fighter was increasingly the most needed version, work on it proceeded the most slowly, due to the extra work involved in developing the different fuselage nose and pressure cabin sections, and only four examples, including the prototype, were produced. The prototype (Ju 388 V2) was the only one of the four machines to receive the tail barbette, but the forward-firing armament of all four machines was the same. This comprised two 0.787 in (20 mm) MG 151 machine guns and two 1.18 in (30 mm) MK 103 cannon in an offset ventral fuselage fairing. An aerial array was mounted on the nose for FuG 220 Lichtenstein radar equipment, and a crew of four was carried. The tail barbette, omitted from the three Ju 388 J-1s built, was to have been fitted to subsequent machines beginning with the Ju 388 J-2.
The first major modifications were planned for the Ju 388 J-3, which was to have Morgenstern radar equipment with much shorter aerials slightly protruding from a pointed, wooden nose cone, and also two extra M G 151 cannon in an oblique dorsal Schräge Musik (Jazz Music) mounting. It was also hoped later to equip Ju 388 J-3s with Junkers Jumo 213E-1 engines in place of the BMW 801TJs. The Ju 388 J-4 was planned to have the very heavy armament of two 1.97 in (50 mm) BK5 cannon in a ventral fuselage pod, giving an installation weight of about 2,646 lb (1,200 kg) excluding ammunition. Single guns of this type were used by other aircraft such as the Ju 88 P-4 and Ju 288.
The Ju 388 was used in tests with the Henschel Hs 298 and, later, the very promising Ruhrstahl X-4, both these air-to-air missiles being scheduled for use with the Ju 388. Because of its high performance, many roles were planned for the Ju 388, and it was one of the aircraft proposed to tow an unpowered Messerschmitt Me 328 glider fighter up to altitude or to piggyback a powered Me 328B bomber to the target area.
The proposed Ju 388 M-1 was to be similar to the Ju 388 K-1 type but with an ETC 2000 rack instead of the ventral bomb housing to enable a Blohm und Voss L10 Friedensengel torpedo to be carried. The L10 consisted of a normal LT 950 torpedo fitted with wings and tail unit to enable drops to be made at greater altitudes than normal. Some Ju 388 M-0s were under construction, but these, together with the projects, were too late, and by the time the war ended only a small number of Ju 388 L reconnaissance machines had seen any operational service. In all the various roles planned for it, the Ju 388 would have been a good match for most Allied aircraft, but only about 200 examples were built, the majority of which were fighters.