Is there an in-setting explanation for how dragons breathe fire?

Question

I'm currently in the process of writing a new campaign setting in which many classical mythical creatures have been rendered extinct for various reasons, one such creature is the dragon.
My initial idea was that some sort of event or evolutionary flaw in the past stopped dragons being able to breathe fire, making them far easier for adventurers and dragon hunters to kill off, similar to how the Dark Souls series made dragons extinct by removing their scales (the things which made them immortal), perhaps a plague removes the dragons' ability to breathe fire, weakening them?

In an attempt to make this less jarring to players than just saying "they get ill, no breathe fire now", I'd like to base the effect off of dragon lore that exists across the various editions of Dungeons and Dragons. Is there any in-setting lore explanation for why dragons breathe fire/acid/(insert damage type here)?

I know 5e is particularly sparse in dragon-lore, so I'm hoping some veterans from older editions might know more about these classical creatures!

Answer 1

Dragons have a special gland which generates the breath weapon

According to the D&D 3rd edition sourcebook Draconomicon (2003), chapter 1, a true dragon's breath weapon is produced by an organ in the chest known as the draconis fundamentum.

The draconis fundamentum (7) is a gland possessed only by true dragons. Attached to the heart, it is the center of elemental activity inside the dragon's body. All blood flowing from the heart passes through this organ before going to the body. The draconis fundamentum charges the lungs with power for a dragon's breath weapon and also plays a major role in the dragon's highly efficient metabolism, which converts the vast majority of whatever the creature consumes into usable energy.

The dragon converts energy taken from its diet into the breath weapon by means of this organ, which generates the breath weapon deep inside the dragon's lungs. The dragon must first inhale deeply, and then, if sufficient energy is available, it can exhale and produce the breath weapon.

D&D 3e asserts that a dragon's breath weapon is supernatural, and won't function in an antimagic field or similar. D&D 5e's FAQ v2.3 p.17-18 disagrees, saying that while dragons are innately magical, the breath weapon is merely part of the background magic that is part of the physiology of many D&D creatures. Either way, however, both editions agree that there's something magical about the dragon's physiology.

Given this lore, there are plenty of reasons why a dragon might be unable to use its breath weapon. Ecological disaster or overcompetition from a high concentration of other dragons in this area might make it difficult for the dragon to feed sufficiently to get the energy for its breath weapon. An illness might make its lungs or draconis fundamentum fail to work properly.

A very Dark Souls explanation might be that most of the the remaining dragons in this world are merely lesser dragons, a mere distant relative of the original true dragons, and as a result they lack the draconis fundamentum necessary to use a breath weapon; according to Draconomicon, this distinction also occurs in D&D between dragons and the other dragon-type creatures like drakes.

Answer 2

Dragons being able to breathe elements is an innate magical ability

Dragons are inherently magical creatures, which is why their bodyparts are so sought-after for alchemy and magic item crafting. Being able to breathe fire is only one of the things that is magical about a dragon, most Red Dragons who can breathe fire will also be able to control fire in other ways as they age. It's something that stems from the magic flowing in their blood.

As Quadratic Wizard points out in his answer, the Draconomicon went into further details about the specific gland that allows dragons to convert food into energy they can breathe, but this in itself also seems to be a magical ability of sorts. Dragons have even been able to show the ability to eat magical items when they're desperate enough, and that will temporarily give them benefits associated with that magical item.

A Sorcerer with dragonic blood will also learn to breathe fire/acid/whatever based on their specific blood, which might suggest that even a dragon without the draconis fundamentum dragons might still be able to produce their breath attacks. (There are, after all, also Dragons that aren't 'True Dragons', that still have breath weapons.)

Whatever lore you're going with, the most likely reason for a Dragon to lose its ability to breathe fire is some sort of magical reason. Perhaps a powerful enough wizard in the past experimented with the Weave and their experiment backfired. As a result, Dragons were no longer connected to the weave through their blood and rapidly lost their supernatural abilities.