It seems to me that the only way to kill a Jax that stacks HP then goes to Atmas is with spell damage.

The problem is when Morgana shields him all game.

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I'm not a pro and maybe I'm just making mistakes when trying to counter this setup, but I can't figure out any way to beat this combo.

kill morgana, kill jax while morganas dead

Be Ryze, explode the spell shield second in 1 second. Enjoy.

It's really not realistic to run through jax to get morgana especially since morgana is not a hero that needs to stay near the fight all the time. Running to her while she has support is near insane since she can cast her cc on you. And you are most likely behind the front line at this point with their team focusing fire on you.

As for Ryze, his spell is very situational. If there are creeps around, good luck with the ult. If jax has boost, again, good luck. This is not to mention that you have to get way too close to him for the ult to bounce back between you two. You will no doubt get destroyed faster than your ultimate kills the spell shield. Not to mention you actually need a ryze to do this.

The shield's only shortcoming is it's range, though--if Morgana wants to keep it active on Jax she will have to be at least close to the fight.

There are counter's to everything.