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Multiple realities
(covers information from several alternate timelines)

A vaccine being administered

A vaccine was a chemical preparation that instructed a healthy immune system how to fight a pathogen. Some vaccines were made of live bacilli, which had to be shipped in a stasis field. (TNG: "True Q")

Sometime around 1960, scientists on a planet exactly like Earth developed the life prolongation complex. This was a series of viruses that became fatal when the infected individual entered puberty. In 2266, Doctor McCoy successfully developed a vaccine that cured at least the fatal form of the disease. (TOS: "Miri")

This would go beyond the capabilities of what is currently understood to be a vaccine, which need to be administered before patients become affected.

In 2004, the Xindi-Reptilians who were gathering individuals of various blood types to create a bio-weapon explained away their activities to Loomis by claiming they were working on an experimental vaccine for which they did not have approval. (ENT: "Carpenter Street")

Dr. Phlox administered a Rigelian fever vaccine to the entire crew of Enterprise NX-01 in 2152 after Crewman Fisher came down with the disease, in order to prevent an outbreak. Around a month later, this ended up saving the life of Ensign Travis Mayweather. Mayweather was abducted by the automated repair station repairing Enterprise, which intended to use his synaptic pathways to enhance its computer core processing power, and replaced with a facsimile designed to mimic a death from isolytic shock. Phlox realized the replica was not Mayweather when he noticed that the microbes from the vaccine, which should have thrived on isolytic energy, were dead. Jonathan Archer and T'Pol were able to rescue Mayweather from the computer core before the brain damage became irreversible. (ENT: "Dead Stop")

In the alternate reality McCoy gave Kirk a vaccine for a viral infection spread by Melvaran mud fleas to which Kirk had a bad reaction resulting in swollen hands and numb tongue, which hindered his attempt to warn Uhura about a possible Romulan attack when Nero attacked Rura Penthe in 2258. (Star Trek)

A shipment of highly perishable vaccines was among the medical equipment destined for Theta VII. (TOS: "Obsession")

In 2364, Ligon II had a vaccine to cure Anchilles fever, which the population of Federation planet Styris IV was suffering from. The USS Enterprise-D was sent Ligon II to negotiate with Lutan, leader of the Ligonians, to acquire the vaccine. (TNG: "Code of Honor")

In 2365, Hester Dealt speculated that a vaccine for the mutated strain of plasma plague might never be found. (TNG: "The Child")

Retroviral vaccines in combination with bio-mimetic gels could create a biogenic weapon. (TNG: "Preemptive Strike")

During the 24th century, radiogenic vaccines which protected against radiation were also available. (VOY: "Inside Man")

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