Honestly it's a nightmare because it's very momentum based. You can't let Kotal touch you, and you have to manage your meter very well.
I hate this MU because its very momentum based like Noob Saibot, in the sense that Kotal does so much damage, that one touch is all it takes. Kotal can then just sit in the sun (especially in the corner). Against Aztec, he uses the kat against me and this especially means you can't run away all game, but the disgusting thing is that you can never throw a Katar at Kotal without meter. He can duck it, and either use F2 combined with good wave dashing to full combo punish.
I also want to mention that Kotal's cmd grab will straight up punish you for trying to water parry, and his d3 will low profile all of Rain's mids except d3, much like Cetrion's.
What you can do:
Check him after MB disk with AMP Katar.
Kotal doesn't have a fast mid so you can always try to check him with a d1 or d3 and his only real threat is poking you back. You can just block that, throw or swing at him again.
Know that Kotal's F2 is the button he's looking for. Practice flawless blocking it in neutral and after Rain's strings with Pushback like b212 so you punish him for trying to get his turn back. Again, meter management is key.
IF you do get a life lead, he'll most likely try to set up the sun and hide behind it. With good movement, you can get in on him quickly and round house kick him right out of the sun.