Honestly you should develop this guy more, as he could be cool but we don't know much about him. For example, he is from both Mt. Targon AND Zaun, which seems very odd. A mystical mountain and a futuristic slum city usually don't mix.
Anyways sense the vast majority of your concept is just a kit, I'll look at that.
Every time he loses 20% of his max HP, his next basic attack gains 300 range and affects other units in a cone (250 to 350 units (scaling on level)) deals 10/lvl (+10% Max HP) (+20% AP) magic damage and slows them by 10% +(1% per 150 Max HP) for 1.2 seconds.
(This effect stacks for more damage/slow if he loses 40%+ max HP in a short period).
Besides the fact this passive doesn't fit at all, in several ways, it is really overloaded. It has AoE damage, a slow, bonus damage, AND bonus range. That is a lot for a single auto attack empowerment.
The ability doesn't seem to fit either. In order to successfully get a chunk of his damage off, he has to eat a bunch of damage. This passive encourages him to not build tanky. This passive also doesn't fit a utility caster who excels at saving many allies at once.
In addition, Crunes can't manipulate or control his passive besides running into damage.
Thematically, it doesn't make sense. Crunes seems to be some mystical caster who bends reality and time to aid his cause, however his power shouldn't rely on him taking damage. This ability doesn't even fit a "Guard" champion as his subtitle would suggest, because its not like he's taking damage for his allies.
I'd rework this ability into something that actually synerigzes with Crune's kit and defines him as more than just a utility caster.
Distorts space in a target area. That area becomes incresingly unstable, slowing and damaging (ticks every 0.5 sec) enemies more the longer the area is active.
Every 1.5 seconds the stages of the distortion goes up a tier.
1: 20% Slow - 20/40/60/80/100 (+10% Bonus HP) (+20% AP) magic damage over 1 second.
2: 40% Slow - 40/60/80/100/120 (+15% Bonus HP) (+30% AP) magic damage over 1 second.
3: 60% Slow - 60/80/100/120/140 (+20% Bonus HP) (+40% AP) magic damage over 1 second.
4 (happens only if a tier 3 happens over a distortion): The distortion explodes, stuning enemies for 1.2 seconds and dealing 90/120/150/180/210 (+25% Bonus HP)(+70% AP).
This ability is solid. I can't ever see it's stun getting off because its got a 6 second delay. I
In general this ability is okay, but its nothing special or unique. And honestly, for a time bending sorcerer from Targon, or whatever Crunes is, it'd be nice to see something a little less generic.
The duration on this ability is also far too long. There is no need for it to be so long. If someone stood in it for 6 seconds, their either dead before that time due to the damage, cc, and ally damage or they've escaped because its only a slow.
Passive: Every time he cast a spell, he gets a 80/100/120/140/160 (+80% AP) shield for 2 seconds.
Active: Creates a wall-like distortion. Skillshots that pass through it are slowed and its damage reduced by 20/22.5/25/27.5/30 %. Seeker-projetiles (such as autoattacks), are slowed and weakened by the same amount and stop seeking their target and continue in a straight line (can still hit the original or another target).
The passive only having an AP scaling DOES encourage him to not go full tank. I wouldn't worry too much about full AP Crunes being too effective because he only has a few sources of magic damage.
The active is far too powerful. This is actually insanely powerful. Its going to pretty much be a Yasuo windwall. Slowing projectile speed is extremely powerful, especially when most abilities are balanced around them. And causing auto attacks to be skill shots not only makes things awfully confusing, but also removes the reliability ADC's are supposed to have.
This ability is just too strong.
Places a mark on the ground that becomes active after a delay.
Up to 2 Marks can be in the map at the same time.
If a mark is set at more than 3000/3500/4000/4500/5000 units-distance of the previous one, the previous one vanishes.
When 2 marks are active at the same time, ANY champion that steps on one is teleported to the other.
Another broken ability. All Crunes has to do is place one of these at T2 tower and another in the middle of bot lane, and whenever things become dangerous have him and his adc pop under tower.
If enemies follow, their not only under tower but Crune and his ADC are prepared. Crune's E is so exceptionally powerful at saving his allies and himself, its more than ultimate levels of utility.
You really need to develop the descriptions more. Because this ability has almost no, if any, counterplay. To my knowledge, you can't destroy it, it lasts forever, and it has no cooldown per mark, person, or use.
When cast, marks an area around him that "remembers" the HP of allies that are nearby when it was cast.
After 5 seconds are allies that are still, or went back to that area get their hp set to the hp they had when cast.
Reduce by 4 seconds the cooldown of his basic spells by every allied champion healed (including self).
And you just made an ultimate that, in nearly every possible way, outclasses another ultimate. The only way Kindred's ultimate would ever be better than this one, is because you can keep fighting when you should die. Crunes otherwise does everything Kindred's ult does, but better with less risk and more potential healing.
Pear this ultimate with Redemption and you would have massive team wide heals.
You can't even try to burst down target's effected by Crune's ultimate, because they will get their health reset and be resurrected anyways.
You've got a lot of real cool ideas, that could be neat in a vacuum, but they don't all fit together. It seems like you tried to shove too many mechanics in at once.
I would go back over Crune's and try to identify why he would be picked, what his strengths and weaknesses are, what specifically does he offer to his team, and add some synergy.
Currently Crune's has no combos or synergy between abilities. All he can currently do is just place a Q ontop of an E and try to bait an enemy champion to follow him through right as the Q stuns them.
You should give him some reason to use his abilties in a certain order or fashion. Bard can portal through a wall than stun an enemy who walked through. Alistar can dash and knockup an enemy together. Tahm Kench can flick a target into his mouth with his Q>W combo. But Crunes doesn't have any of that.
I really suggest you develop you ideas more. While Crunes is absolutely OP, champion concepts aren't easy to make. They can be really fun and you have a lot of potential for Crunes.
If you have any questions, feel free to ask. I hope my feedback helps!