They were biologically-immortal demigods who remained sequestered in the Sacred Realm, but would occasionally return to Hyrule to protect it in instances of extreme danger. They could take damage, feel pain, be killed, but could not die of old age or disease.

So a controversial recurring fan-theory from Legend of Zelda (especially in the Ocarina of Time lore) is that the sages – Saria, Darunia, Ruto, Impa, and Nabooru – were killed in their respective temples, and were awakened as sages who were essentially ghosts. I don’t believe this is the case. Rather, a more likely explanation is that when a sage is awakened, they would spend eternity in the Sacred Realm similar to gods in Greek Mythology living in Mount Olympus. They were assigned to remain there and protect the Triforce; they would occasionally warp to their temples to oversee them to ensure evil does not infiltrate them, but would usually only appear in Hyrule proper in instances where their help was truly needed.

I think the sages had god-like powers and superhuman abilities, and could not die of old age or disease. However, they could still be attacked, feel pain, take damage, become disfigured, take their own lives, or be killed. Under normal circumstances, the sages would technically be able to live forever without aging – assuming they remained within the Sacred Realm – but throughout Hyrulean history, occasionally the sages would reemerge among the mortal world to protect its people. And during these instances, sometimes the sages would have been killed in battle against evil forces.

For example, I don’t think the sages were special referees who watched down on the people and made them play nice whenever there was geopolitical turmoil. Like, if Hylians went to war against Gerudo, the sages wouldn’t beam themselves down, snap their fingers, and magically make everything peaceful. I think however, in extreme instances where Hyrule was attacked from outside forces such as evil monsters, the sages would emerge and assist the people in a war against darkness. Maybe in these kind of scenarios, sages could have been killed, and their replacements would be awakened in later years.

Let’s pretend that prior to Saria becoming a sage in OoT, in like 35 years before the start of the game, Hyrule was invaded by an army of Stalfos warriors. The people of Hyrule tried to fight off the invaders, but were overwhelmed. An army of Stalfos besieged the Forest Temple, where the previous Forest Sage was dispatched to protect it, but was sadly killed by the invaders. This meant the Forest Temple was without a sage for several years until Saria was awakened as the chosen one.

So again, I really don’t think the sages were all dead and that they were all ghosts in the Sacred Realm. When awakened as the chosen ones, they probably were just given god-like powers such as semi-immortality, flight, levitation, teleportation, and shooting beams of magic from their hands – but could otherwise be susceptible to physical harm and even death at someone else’s hands. Rauru was just lucky and never took damage from outside forces during his years as a sage, whereas the previous sages were killed throughout history prior to the start of OoT.

I think that prior to the events of OoT, the original five sages were all killed for various reasons, such as maybe a war against evil forces. Maybe the five were killed whilst trying to protect the Triforce from Ganondorf around the time when Kid Link entered the Temple of Time, or during Ganondorf’s reign of terror. Rauru perhaps evaded harm or was spared. Then when Adult Link’s quest began, the new sages were destined to be awakened by him.

At the end of the game during the credits, Mido and the Zora King weren’t mourning the deaths of Saria and Ruto: they were just depressed that they wouldn’t see them very often or again whatsoever, as the sages were assigned to remain in the Sacred Realm or their respective temples, unless of extreme circumstances when the world needed them.

Saria technically could randomly warp to Kokiri Forest and wave at everyone and say, “Hey guys, I’m still alive! Who wants to play kickball!?” – it’s just that she wasn’t supposed to do that, as it was mandatory for her duties as a sage to protect the Triforce, oversee the Forest Temple, and to protect the people of Hyrule in instances where outside forces overwhelm them.