Aftershock is the runeset you will be taking for most of your games on
Nautilus, but
Phase Rush is too good of an option to pass up on in certain matchups and can make a very difficult game feel a lot more playable; even then, I wouldn't recommend running it every single game due to it being famous for creating bad habits, and also for having less synergy overall with
Nautilus' kit and purpose.
Aftershock Runeset
Aftershock: It will grant you a considerable amount of extra
Armor and
Magic Resistance every time you apply hard
Crowd Control on any champion, which will happen effortlessly since
Nautilus'
Auto Attacks,
Dredge Line and
Depth Charge all activate it. The bonus will only increase with bonus resistances provided by items, and its burst of damage increases with your bonus
Health, making it a perfect fit for the tank playstyle.
Shield Bash: The shield from
Titan's Wrath provides a consistent enough source of shielding to activate this rune, for a small bonus to your damage and survivability during fights. Also synergizes well with other elements in this setup that scale from bonus resistances, such as
Conditioning and
Jak'Sho, The Protean.
Conditioning: At the 12 minutes mark, you will gain bonus
Armor and
Magic Resistance with no further input from you, and will also gain small bonuses to any amount of said stats you gain from items and other sources such as the
Mountain Dragon. This effectively translates to bonus gold value from all of your purchases, and becoming tankier passively throughout the entire game on a condition that you will meet 99% of the time anyway.
Unflinching:
Nautilus applies a lot of
Crowd Control, but he is also the target of it very often. When this happen, this rune allows you to gain extra resistances that remain after the
Crowd Control effects have worn off, making you more apt to survive during the fight and keep moving around.
Additional notes:

Spoiler: Click to view
Note that any form of
Crowd Control will activate this effect, including
Slows; and since all members from any given team is bound to get the
Red Brambleback buff lategame, which
Slows targets being hit by an
Auto Attack, this rune is extremely consistent since almost every game is guaranteed to have people applying
Crowd Control on you regardless of composition.
Magical Footwear: You will gain
Slightly Magical Boots through normal gameplay, and even quicker into the game if you pull off any successful ganks or
Jungle skirmishes early in the game. Saving 300 gold on
Boots while also getting an extra 10
Movement Speed out of them is simply too good for almost every
Jungle champion in the current meta to pass up on.
Approach Velocity: All
Crowd Control applied on enemy champions either by yourself or your team will provide you with a small but useful boost to your
Movement Speed, which will be easy to upkeep thanks to
Nautilus' endless amounts of it. This will prove the most useful when you are trying to stick to a target that is dashing away from you while your abilities are coming back from cooldown, and also when executing
Ganks when one of your laners has
Crowd Control by themselves.
Phase Rush Runeset
As for the
Sorcery tree, in the games where you go with
Phase Rush:
Phase Rush: It's the reason we take this tree in the first place. The burst of
Movement Speed offers really high value even in situations where you wish to keep fighting in close range because you will find it much easier to dodge skillshots, chase, flee or reposition, as the situation sees fit.
Nimbus Cloak: Taken mostly because it's the only good choice among all the options in this slot. A small burst of
Movement Speed every time you use
Smite can come in handy, but the bonus after you use
Flash can be really noticeable when you are using it defensively, or if you need to cover any extra distance after flashing.
Transcendence: You will naturally gain 10
Ability Haste through normal gameplay, which is valuable since it increases the amount of times you get to use
Riptide while farming, and also decreases your downtime after you have engaged on targets with
Dredge Line. The cooldown refund on takedowns part of the rune is largely irrelevant otherwise.
Waterwalking: You will be spending a considerable amount of time during the game crossing the river as a
Jungler, so getting extra
Movement Speed while you're on it is only the right choice. The bonus stats will make a considerable difference when you're taking an objective on your own, and also if you find yourself fighting with the enemy
Jungler over an objective or the
Rift Scuttler, especially the very first one that appears at 3 minutes 30 seconds into the game.
Conditioning and
Unflinching are taken with this setup for the reasons already explained above, but also because I find that they offer the best value as secondary runes, since no combination you could make with the
Inspiration or
Precision trees could offer as much value with so little player effort involved.
Rune shards: +8
Ability Haste and two scaling
Health shards are the best for making your early game clears quick while also not giving up on mid and late game prowess. You could swap one of the
Health shards with the one that grants a flat +65 bonus to it if you wish for a quicker first clear, but I find it largely redundant given how quickly
Nautilus can clear the
Jungle in the current patch without it.
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