This page contains information regarding new Star Trek material, and thus may contain spoilers.
In the alternate reality, the advanced long-range torpedoes were a type of photon torpedo developed by Starfleet in 2258 as part of the preparations for a war with the Klingon Empire. (Star Trek Into Darkness)
The advanced long-range photon torpedoes had several classifications. The torpedoes were classified as Class 12 photon torpedoes in the interior security screen and CVN-65 Mod.PHO 453 on the detonator processor access panel. They were called Mark VI and CL 365-A photon torpedoes on several computer screens. On the torpedo casings they were marked as PHOT1093 torpedoes. Each torpedo also included a unique serial number such as CF-6660, CS-7200, MC-9321 or RA-4401. They operated at a core temperature of 323 degrees celsius, and had the explosive yield of 320 isotons and the explosive range of 300,000 kilometers. (Star Trek Into Darkness, display graphics)
The long-range of the torpedoes made it possible, for example, for a starship to launch them from the edge of the Klingon Neutral Zone and impact on specific cities and locations on Qo'noS, the Klingon homeworld. A classified feature of the torpedoes was that they were designed to be untraceable and undetectable to Klingon sensors. While transporters could lock on to the torpedoes and transport them, the inner casing shielded the interior fuel compartment and warhead payloads from scanners. The warhead was active at all times and could not be accessed directly. To access it, the fuel compartment needed to be opened. To prevent unauthorized access and tampering, the torpedo was programmed to arm itself and automatically detonate in 30 seconds after unauthorized access was detected. The torpedo was protected against attempts to re-rout the detonator processor and against cutting the fiberoptic cables in its circuitry. The detonator processor could however be manually removed to disarm the warhead. (Star Trek Into Darkness)
The development of advanced long-range torpedoes was one of the advanced weapon system programs overseen by Admiral Alexander Marcus, in his secret initiative to militarize Starfleet, following the destruction of Vulcan in 2258. Section 31 oversaw the development of this weapon system by Khan Noonien Singh. Khan secretly retrofitted 72 prototype torpedoes to carry the surviving crew members of his old ship, who were held hostage by Admiral Marcus. He intended to smuggle them out from Section 31, but his plan was discovered.
When the London Section 31 facility was bombed in 2259, the torpedoes stored there were destroyed in the explosion. None of them were the torpedoes modified by Khan. Admiral Marcus supplied the USS Enterprise with those 72 retrofitted torpedoes and ordered Kirk to fire them at Khan who was hiding on the Klingon homeworld. At this time Marcus also erased all information on the torpedoes from official records. Marcus sabotaged the Enterprise, so that the ship would be disabled at the edge of Klingon space. The plan was for the Klingons to discover the Enterprise and in response to the torpedo attack, start a war with the Federation.
The torpedoes and their tubes were loaded on board by CMUs through the Enterprise hangar deck when the ship was docked at Starbase 1. Because Chief Engineer Montgomery Scott was denied access to the classified specs of the torpedoes, he refused to authorize the installation of the torpedoes on board. He feared that when launched, the torpedoes could cause a subtle shift in the magnetic output of the warp core. This would lead to a catastrophic radioactive leak and a chain reaction that would kill the entire crew of the Enterprise. When Kirk ordered Scott to sign for the new weapons anyway, Scott resigned his commission.
Afterwards, these torpedoes were stored in the starship's weapons bay. Kirk decided to disobey his orders and didn't fire the torpedoes. The secret plans of Marcus and Khan were uncovered by the crew of the Enterprise. After commandeering the USS Vengeance, Khan demanded that Spock turn over the torpedoes to him. Spock obliged and allowed Khan to beam the torpedoes to the Vengeance. Before this though, Khan's crew was removed from the torpedoes and the detonator processors were programmed to detonate the torpedoes after transport. The resulting explosion crippled the Vengeance and heavily damaged the Enterprise. (Star Trek Into Darkness)
In 2263, the Enterprise still carried advanced long-range torpedoes among its weapons compliment. During the battle of Altamid, the Enterprise fired one tactical torpedo, though it proved ineffective as the swarm moved around the torpedo, causing it to fly off into space. When the ship was fatally damaged by Krall and his forces and the crew forced to evacuate, Montgomery Scott – pursued by Swarm drones – escaped the Enterprise by hiding inside a long-range torpedo and firing it into space. Controlling the torpedo from within, Scott piloted it into the atmosphere of Altamid where it crash landed on the planet's surface, nearly sending the Starfleet engineer over a cliff. (Star Trek Beyond)
The advanced long-range torpedo was designed by Chris Ross. John Eaves, recalling initial work he and Ross did as the designers on Star Trek Into Darkness, stated, "Chris was working on special torpedo designs that would eventually take up most of his time on the film due to the thousands of intricate changes and details to be worked out."  The term "advanced long-range torpedo" was used by Hikaru Sulu in the film. Doctor Leonard McCoy called one of the torpedoes a four-ton stick of dynamite, suggesting an approximate weight of the torpedoes.
The smaller prime reality version of the Mark VI photon torpedo was seen in Star Trek II: The Wrath of Khan and Star Trek III: The Search for Spock, where they were similarly modified to carry people, though in that case as a coffin to launch the corpse of Captain Spock to the Genesis Planet. The 300,000 kilometer range was similar to the weapons range established in TNG: "The Wounded" for photon torpedoes used by the USS Phoenix in 2367 in the prime reality.
A Section 31 weapons summary computer screen at the advanced weapons development facility in London stated, that a weapon system designed by Section 31 fell within treaty specifications banning cloaked and preemptive weapons as the stealth function was activated via remote capability after launch. The remote stealth capability was a classified feature of the weapon that was to be disclosed at the discretion of the theater commander to the captain and first officer of a participating vessel. While the chief engineer was normally given full detailed specifications of any cargo carried on board a starship, Section 31 also gave the theater commander the authority to make the decision if he wanted to disclose such information on the torpedoes to the chief engineer. While the weapons summary did not specifically state it was about the advanced long-range torpedo, the torpedo was a weapon system being manufactured at the facility at the time, and it had these or similar properties. Treaty specifications banning the use of cloaked weapons suggests that an earlier treaty similar to the Treaty of Algeron existed in the alternate reality.
Some aspects of the torpedoes were further explained in the novelization of Star Trek Into Darkness. Before being deployed to the Enterprise, the new torpedoes had only been tested in computer simulations and in them had functioned as intended. Kirk's mission would have been the first real combat situation for the weapons. The advanced torpedoes, like all other photon torpedoes ran on their own miniaturized drives. It was this new drive system that rendered the torpedo untrackable. In the prime timeline, techniques and technologies to suppress a warp signature and hide the warp trail like this existed in the 2370s, such as obscuring the signature with a gravitational field or by remodulating plasma injectors, and hiding the trail by dissipating it with a magneton pulse or masking it with a randomized EM field. These were mentioned in Star Trek: First Contact, VOY: "Warlord", "Dreadnought" and DS9: "To the Death".
According to the novelization, the drive compartments were shielded and sections normally open to inspection and repair were combination locked down. Scott was more specifically concerned that when the drive of one of the torpedoes was activated, it would interfere with the drive of the Enterprise. If the new drive system was more powerful and differently configured than in the model used on the Enterprise, a more powerful drive would use more powerful magnetic containment fields for the intermix. It would generate a greater magnetic field shift when activated, than in any earlier model. A field of that magnitude would create an interaction with the main core’s containment fields and any such interference would be catastrophic.
When Spock confronted Dr. Carol Marcus on the weapons bay about her identity, she was verifying that the internal guidance systems of the torpedoes were online and updated with the latest celestial mapping coordinates as they were going to be utilized in non-Federation space. Coordinate targeting of the torpedoes was accomplished via automatic geophysical positioning. In the novelization Sulu calls them: "advanced long-range undetectable torpedoes". The 23rd cable down, that McCoy was supposed to cut, connected the internal controls of the torpedo to the detonator. In the torpedoes modified by Khan, the drive unit was reduced in size to make room for the new compartment and a portion of the on board stored energy meant to maintain the weapons electronics and related systems was redirected to sustain the cryotube. Spock, with the help of McCoy, only tripped the self destruct of one torpedo manually before they were all beamed to the Vengeance. The plan worked because Khan didn't have time to scan all the torpedoes before the armed torpedo detonated and caused a chain reaction detonation of all 72 torpedoes.
The video game Star Trek D-A-C, set between the two films in the alternate reality, also features similar advanced weaponry on Federation starships, such as seeking missiles, quantum torpedoes and charged projectiles.