The Navy began the program by testing and reverse engineering two captured Type XXI U-boats: U-2513 and U-3008. That analysis led to four goals: increasing the submarines' battery capacity, streamlining the boats' structures, adding snorkels, and improving fire control systems. The Navy immediately focused on designing a new class of submarines, but the Bureau of Ships believed that the vast fleet of existing Gato, Balao, and Tench class submarines could be modified to incorporate the desired improvements. In June 1946, the Chief of Naval Operations approved the GUPPY project. The initial two boat test program, implemented by the Portsmouth Naval Shipyard, eventually grew into several successive conversion programs. Those upgrades proceeded in seven variants: GUPPY I, GUPPY II, GUPPY IA, Fleet Snorkel, GUPPY IIA, GUPPY IB, and GUPPY III. (The apparently out-of-order sequence is correct; see below.) Some boats that went through an early phase were then upgraded further in a later phase.
These modifications changed not only the boats themselves but also their terminology: after a GUPPY conversion, the faired structure around the boat's conning tower and mast supports was called the "sail."
Internally, the boats underwent considerable rearrangement to accommodate larger battery wells and batteries of greatly increased electrical power. The batteries themselves were of a new design. Compared with the original Sargo battery, the Guppy battery used a greater number of thinner plates that would generate higher current for a longer time. However, these batteries had a shorter life, 18 months versus the five years of the Sargo battery, and took longer to charge. They also required ventilation to remove hydrogen gas, and required cooling water to the battery terminals and termination bars. Four 126-cell batteries were installed in enlarged battery wells that replaced former storage, ammunition, and refrigeration spaces. These four batteries could be connected in series or parallel, providing a wide range of voltages and currents, and thus a wide range of speeds.
In the maneuvering room, two or four of the earlier high-speed motors and reduction gears were replaced by slow-speed motors. All open-front switchboards were replaced with enclosed splash-proof cabinets. Lighting and other "hotel" electrical loads were converted to use 120 volt 60 hertz alternating current, and ship electronics to use 120 volt 400 hertz AC. A new air conditioning system of greatly increased capacity was also installed.
In service, these boats offered massively improved underwater performance. Pomodon reached 17.8 knots surfaced and submerged, Odax slightly less.
The GUPPY II conversion (SCB 47), implemented from 1947 to 1951, was generally similar to the GUPPY I, except for retention of both periscopes and introduction of the recently perfected snorkel. The addition of three new masts -- snorkel induction, snorkel exhaust, and ESM mast -- required more room in the upper portion of the sail. BuShips approved two different sail designs:
The "Electric Boat Sail" had a straight trailing edge, round windows, a wider top and a more rounded forward edge.
The "Portsmouth Sail" had a thinner top, curved trailing edge, square windows and a sharper lower forward edge. It was put on all boats which used the government plans for the conversion.
Some boats with a Portsmouth Sail had an SV radar and needed extra room to house the aerial, thus had a bulge at the sail top. Later modifications put the SS or SS2 radars on these and other boats which had a smaller aerial and had an indicator with interlocks which allowed the mast to be housed only with the aerial in certain angular positions. Also, some GUPPY II and GUPPY III boats had their sails extended higher above the waterline, the "Northern Sail", to raise the bridge, allowing it to be manned in more severe weather.
All boats converted during the GUPPY II program that originally had high-speed drive motors with reduction gears had these replaced with low-speed direct-drive motors, producing 2500 horsepower (1.9 MW) per shaft.
The two GUPPY I boats, Odax and Pomodon, were modified to GUPPY II standard.
When the Navy realized that it would not be able to fund all the GUPPY conversions it desired, it devised the Fleet Snorkel program (SCB 47B) as a means of adding the minimum necessary modifications to fleet boats. The Fleet Snorkel modernization added a snorkel, a streamlined sail, a higher capacity air-conditioning system, and a more powerful electrical system. The deck guns and auxiliary diesel were removed. Unlike the GUPPY conversions, the Fleet Snorkel boats retained their original deck structure, bow, and storage batteries. Submerged performance of the Fleet Snorkel boats was therefore significantly inferior to any GUPPY conversion. Despite their limited features, the Fleet Snorkel boats served almost as long as the more modern GUPPY boats. Three boats, Piper, Sea Owl, and Sterlet, received a large BQR-4A bow sonar.
The GUPPY IA program was succeeded by the nearly identical GUPPY IIA program (SCB 47C), implemented from 1952 to 1954. The GUPPY IIA, however, further alleviated the cramped internal conditions of earlier conversions by removing one forward engine and replacing it with pumps and air conditioning machinery. Some boats had the high-pressure air compressors relocated to the lower level of the forward engine room. The freezer and refrigerator units were moved to the space under the galley, and the sonar room was relocated to the forward end of the pump room. Sargo II batteries were installed in the existing battery wells.
Externally, the GUPPY IIA differed from the GUPPY II and IA by having only three diesel exhaust outlets, whereas the earlier conversions had four.
The GUPPY II conversions suffered from very cramped internal conditions due to the four-battery configuration. The GUPPY III program (SCB 223) was devised to address this problem. In 1959, , became the prototype conversion. She was cut in half and lengthened with a 12.5 foot (3.8 m) section forward of the control room to create space for a new sonar room, berthing, electronics, and storerooms. The removal of the sonar room from the forward torpedo spaces allowed an increase in the number of reloads. Crew spaces were also refurbished. As in the GUPPY IIA conversion, one diesel engine was removed.
From 1961 to 1963, eight more GUPPY II boats were upgraded to GUPPY III standard. These boats differed from Tiru by adding a 15 foot (4.6 m) section forward of the control room. They also retained all four diesel engines. This increased the boat's length to and raised surfaced displacement to approximately 1975 tons.
All boats received the BQG-4 PUFFS passive ranging sonar, identifiable by the three fin-like sonar domes added to the superstructure. The conning tower in the sail gained an additional five foot (1.5 m) section to accommodate the Mk 101 fire control system and Mk 37 director. All GUPPY III boats received a plastic sail.
The GUPPY III conversion was part of the Fleet Rehabilitation and Modernization (FRAM) program. All 24 GUPPY II boats were originally slated to receive the GUPPY III upgrade, but budgetary constraints limited the program to a total of nine boats. Despite their extensive modifications and upgrades, the GUPPY III boats served only slightly longer than the rest of the GUPPY fleet.