YMMV / Quantum Protocol

• Nintendo Hard: All dungeons after the first have enemies with effects that can easily disrupt your strategies along with very tanky and tricky bosses. Even the Purposely Overpowered Checkmate deck will struggle with these enemies if the player cannot figure out the best strategy.
• That One Boss: Zirus is the hardest main story boss due its two arms. Each arm already has boss level HP on their own, meaning the player will have to defend against attacks from all three body parts. The arms aren't simply beatsticks either, since they can do things like summoning fast and powerful minions, forcing the player to discard their hand, summoning an unhelpful mook to the player's field, and dealing 1 damage to all player cards. Zirus itself uses a multihit attack that gets stronger as the player reprograms, on top of negating every other hit. For many decks, Zirus is considered harder than the actual Final Boss due to how many effects and attacks the player has to keep track of. The August 2021 patch nerfed the Zirus by increasing the cooldown of some of the arms' effects.
• That One Level: For story dungeons, the Undertow can be considered very difficult, even discounting that Zirus is at the end. The enemies have deck milling mechanics and hand discarding mechanics, which means they can easily send the Reprogram card to the trash, forcing the player to waste valuable turns trying to get it back. The BlackVirus enemies can attack the player's HP directly and transform any card that damages them into a copy of themselves. While other stages are hard in their own ways, they're still easier to manage since they lack methods to get around the player's Reprogram card.