Initially, everyone in Red Algorithm had the same starting position. Each hero had his bonus, but then everything depends on your skill and RNG. Like in chess, a grandmaster who played the game for 10 years had the same pieces on the board as someone who just learned the game an hour ago. It was a good and fair system. Everything changed in version 1.3 when runs were introduced.
With runes, you can improve the stats of each hero 10 times per stat. Usually, 1 invested rune would give a hero +1% to the stat (like +1% to damage), but in some cases, the numbers are a bit different. A few runes won't make the hero much stronger, but 70, which is the total limit of them, will. There are 13 stats to improve, 10 runes can be invested in each, but you can find only 70 runes and not 130. You can't improve all stats with runes, so you have to choose which to improve, and which you should leave as they are. For instance, John might not need additional HP as he already has an HP boost, but he will definitely benefit from more move speed. At the same time, Sarah might really enjoy a boost in health and some regeneration. Runes are attached to a particular hero and you can't transfer them between them. You also can't reset runes and reinvest them in another way, so be wise when you invest them. The reset button in settings will just erase them all and you won't get free runes after that.
Runes are similar to any bonuses on the map, they just appear there randomly and you should pick them up while monsters are chasing you.
Rune drop rates are mentioned in the game, but the general rule is that your chances of getting a rune are much higher in Hard Mode, and after 15 minutes. Runes can appear on the map only after 4 minutes. You can also see the current rune drop rate if you turn on Dev Stats as the "rdr %" at the end. Also, perk Collector (native to Fernando), increases the drop rate, as well as the total number of completed achievements. Cursed or blessed status of a weapon also affects rune drop rate. Plus, you can purchase Pickaxe DLC on Steam that will increase the rune drop rate by a factor of 2, speeding up the grinding/farming process.
There is also an option that allows you to disable rune effects in settings, so you can play the game the way it was before runes were added. This option is called "Purity" and it's off by default. If you set it to "on" and play in Hard Mode, your best results will be uploaded to a special Steam leaderboard with the same name (Purity), and during that game stat bonuses from runes won't work. Purity is something like a tournament game mode, it makes everyone equal before the challenge.
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