Starting with the fourth one, all secret skills are tied to the Rank Up functionality: the third skill becomes available immediately upon activation, however the next one will require you to rank up your weapon.
To rank up, you’ll first need to complete the story quest “Traces” available on Lv. 35, after which a new questline “Cr. Smelter Tale” will become available. Once it’s completed, the Rank Up tab will be unlocked in the Workshop.
Ranked up weapons have their own stats, which can be increased by charging said weapons with Clarity Potions. Charging is not always successful, but materials are consumed even if the procedure fails. Rank Up stats accumulate and remain active even if the character switches to a different weapon.
Once all stats are maxed out, you can Rank Up the weapon. After that, a new weapon is activated, and the character gains another useful secret skill.
Ranked up weapons can be worn by the character. Simply equip them in the “Skins - Weapon” menu.