Ever since we began our journey on Tutorial Island, we've been casting magic spells with these things called runes. During the tutorial, we were given some air and mind runes to Air Strike the chickens back to Lumbridge. Upon our arrival on Gielinor, we "borrowed" runes from the Magic tutor until eventually we were able to buy them from the Grand Exchange... unless you're an ironman, then you actually had to use Runecrafting to get your runes. So, as a skill in the game, Runecrafting is our main source of obtaining runes. But lorewise, that wasn't always the case. How did the human race actually obtain the power of using magic and runes?
As almost everything, it all began with the Elde... Guthix of course. As you all know, Guthix was the first god to visit Gielinor. Here he found some magical object called the Stone of Jas. Guthix felt like Gielinor was so beautiful, that he wanted other races to live here in peace. So, he brought the humans, dwarves, elves, fairies, gnomes and all the other races we all know and love. Okay, maybe some of the demons came a bit later with other gods. Upon their arrival, Guthix had a brilliant idea to use the Stone of Jas to create runes. He donated those runes to the humans and some of the other races. One can only wonder how much Runecrafting Guthix had done with the Stone of Jas, just to get enough runes for everyone. But as you can already guess, these runes eventually become scarce. Powerful mages fought each other over the runes, the winner taking all of the loser's runes.
During the Second Age, the first runecrafter arrived. The Fremennik Seer V, or hero as he likes to call himself, found the Stone of Jas in the mines on Lunar Isle. He realised that the rocks close to the stone had become what we now call Rune Essence. After some studying, he learnt that these stones had the capability of absorbing magical elements. In order to create these runes, V and his followers created the runecrafting altars. These were positioned in places where the altar was most attuned to their corresponding element. An example of this is the Cosmic altar on Zanaris: since Zanaris is Gielinor's moon, the cosmic energy on Zanaris is very present. As we know from the Lunar Diplomacy quest, the Fremennik didn't like magic stuff, so V and his followers isolated themselves on Lunar Isle and created the Moon Clan. Thanks to this isolation, the craft of creating runes remained a secret to the outside world.
Fast forward to the God Wars in the Third Age. If you thought runes were scarce before, it was even worse at this point. The huge war that kept Gielinor busy drained all of the remaining runes from the people, until at the start of the Fourth Age, magic was lost to all those that required runes to perform magic, outside of the Moon Clan of course. At the start of the Fifth Age, new Rune Essence mines were found in the cold far north. The mines were very difficult to reach, so it was still hard to obtain Rune Essence. Still, when they realised how the altars spread around Gielinor worked, the Wizards' Tower was built. Here, four factions worked together to study the runes and their magic. Eventually, the Red Order apprentice figured out a way to teleport. Sadly for him, he wasn't careful enough with his idea, and the Grey Order stole his idea. During the ritual required to unlock teleportation, the Blue Order found out that a Zamorakian demon was necessary as an anchor and that teleportation went through the Abyssal plane. The Saradominist Blue Order broke off the ritual and an oopsie occurred. The First Wizard Tower burned down and only the Blue and Red Order's apprentices survived. The Blue Order's apprentice Perien built a new tower and became its first Archmage. He blamed the First Tower's destruction on the Red Order and banned them from entering the new tower. Perien and his followers worked on a new version of the teleportation spell, specifically one that would teleport to the Rune Essence mine. This spell was successful and very important, as the long and difficult trek to the Rune Essence mine in the north was no longer needed. Eventually, this knowledge became more public, and we've come to the point where anyone with a pickaxe can get the Rune Essence for themselves. This marked the beginning of the Runecrafting skill.
As the runes represent elements, it's not weird that there's a fire, air, water and earth rune. But as we all know, Runescape has plenty of different runes. For example, the nature rune altar found on Karamja seems to represent Guthix, the law rune altar found on the Saradominist island Entrana represents Saradomin, and finally the Chaos rune altar found in the devastated Wilderness represents Zamorak. Even Armadyl has his own rune, but weirdly enough, they're just called Armadyl runes. The other (non combination) runes represent the human body, cosmic energy, and astral energy.
So, there it is. The origin of runes again shows how greedy humans always have and will be when it comes to resources.