Depending on the direction of Ragnar's movement, weapons can be thrust, swung overhead, or slashed. Repeated strikes unleash a powerful spinning attack. All weapons may be thrown, and deal as much damage when thrown as a melee attack. When Ragnar has killed enough enemies in a short span of time, he enters a brief "Berserk Mode", which allows him to resist damage and hit harder. There is also a special rune which instantly activates Berserk Mode.
Although rather linear, Ragnar does not need to kill everything in sight (common in games of the time) to travel from one level to the next. In some levels, players have found alternative ways of getting through to the next level. However, particular scripted pawns must be activated (killed, moved or tripped) in key zones to initiate certain actions to continue and move the story along.
Rune features several multiplayer modes, typical for the time, such as Deathmatch, Team Deathmatch, and so on. The expansion, Halls of Valhalla, added one unique mode, which is inspired by football; the players are split into team, and score points by dismembering players in the opposing team, picking up their body-parts, and throwing them into the goal. It is a game of spatial orientation in which opponents manoeuvre around each other, swinging in and out of range and attempting to score hits on each other. There are a variety of attacks available to the player at any one time, dictated by the weapon they hold at that moment. The geometries of each swing are immutable - thus players are able to fine tune their movement to the precision of a few pixels, and accurately behead their opponents. Over the years, Rune developed a thriving and competitive clan community, with players from all over the world joining servers, playing together, and forming clans.
The story begins when the player, as Ragnar, is initiated into the Odinsblade, an order of warriors sworn to protect the runestones, magical creations of Odin which bind the evil god, Loki and prevent him from unleashing Ragnarok – the end of the world. Ragnar has completed his initiation by beating the great warrior Ulf in combat, when a warrior bursts into the scene and informs the two that a Viking known as Conrack is leading a raid on an allied village. Ragnar and the rest of his village's warriors are assembled into a longship to do battle.
They encounter Conrack's longship, and Ragnar's father is about to order his men to attack, when Conrack calls upon Loki and destroys the ship with a thunderbolt. The ship sinks, killing all on board but Ragnar, who receives a message from Odin that it is not his time to die. Recovered, he swims to safety in an underwater cave. Ragnar fights his way through the monster-riddled caverns. He eventually enters the land of the dead, domain of Loki's daughter Hel.
Passing through the Underworld and facing the ghastly undead, Ragnar learns the enemy's plan: Conrack's carnage sends many dishonored souls to Hel's domain, who in turn gives them to Loki to transform into an army which will conquer the world. After fighting his way through Hel, Ragnar is captured by goblins and fights their beast in the trial pit. He defeats the beast and escapes goblin lands riding on a giant flying beetle. When he emerges from the caverns, he stands before Thorstadt, the mountain fortress of Conrack, and fights his way through it to a Temple of Loki. Inside, Sigurd – Conrack's right arm – confronts his master about all the destruction and asks him to drop the charade of worshipping Loki. Conrack states that Sigurd has outlived his usefulness, and sends two of the transformed dishonored to kill him, then escapes. Ragnar enters the scene and stands before the dying warrior. Sigurd informs Ragnar that he is the last of the Odinsblade, and saving the world is up to him, then dies.
Ragnar follows Conrack, and ends up in the land of the Dwarves. In Rune, Dwarves are depicted as short, stocky, purple beings. He travels through the industrial powerhouse of the dwarven land and learns that the dwarves are supplying weaponry and armor for Loki's new sinister armies. Odin then tasks Ragnar to murder the dwarf king, whose will holds the dwarves' allegiance to Loki together. The king has apparently proclaimed himself a semi-god, and resides in a great temple dedicated to himself. Ragnar enters battle with the king, and he uses the great machine that gives the king his powers to destroy him.
Ragnar travels deep below the earth and to the castle of Loki himself. Odin tells Ragnar that even he will not be able to contact him whilst he transverses through Loki's realm. Ragnar discovers that it is Loki's blood that transforms Hel's undead warriors to the monsters of Loki's armies. He passes through the castle and Loki's maze, arriving at the holding chamber of Loki himself. It is here Ragnar faces Conrack at last. Ragnar knocks the rogue Viking into a river of Loki's blood, which seems poised to kill him. However, the great stone snake which binds Loki drips acid onto his gaping chest wound and the green blood turns purple. Conrack rises out of the river, reborn in Loki's image as a hideous monster. Conrack reveals to Ragnar that Loki's armies are invading Midgard and destroying Odin's runestones left and right. He escapes with a great leap. After a tussle with some undead, Ragnar dives into the river, emerging as a mighty giant.
Loki tries to persuade Ragnar to join his side. He refuses and goes after Conrack. He escapes from Loki's castle and makes his way through caverns out into the world above. He then stands witness to the devastation wrought by Loki's armies. Loki mocks him, but he presses on. His fellow warriors no longer recognize him, and attack him on sight. Ragnar finally arrives home, only to see it totally destroyed. Loki offers one last time to join him, and Conrack sends his men forward to destroy the runestone and Ragnar. There are two possible outcomes of the game, depending on what the player does here.