There are a few hard counters to Calyrex-S. The notable two are:
Yveltal
Yveltal @ Heavy-Duty Boots
Ability: Dark Aura
EVs: 252 HP / 4 Def / 252 SpD
Careful Nature
IVs: 15 Spe
- Knock Off / Foul Play / Sucker Punch
- U-turn
- Defog
- Roost
YGod! The true god of both Ubers/AG, it's the best counter to it that's very easy to fit. Sporting impressive bulk and a great typing in Dark/Flying makes it a hard counter for Calyrex-S. It's able to plainly OHKO it straight with Knock Off, even on Dynamaxed Caly-S. Knock Off has great utility in removing item, Foul Play hurts set-up sweepers and Sucker Punch is for priority.
Apart from being an Caly-S check, it's very easy to use thanks to reliable recovery. It's also the Defogger generally. Boots ensure dem Stealth Rocks don't annoy, while maximum bulk are needed to tank hits.
Some calculations prove it:
252 SpA Calyrex-Shadow Astral Barrage vs. 248 HP / 252+ SpD Yveltal: 85-101 (18.6 - 22.1%) -- possible 5HKO
252 SpA Calyrex-Shadow Draining Kiss vs. 248 HP / 252+ SpD Yveltal: 96-114 (21 - 25%) -- 0% chance to 4HKO
252 SpA Life Orb Calyrex-Shadow Max Starfall vs. 248 HP / 252+ SpD Yveltal: 250-294 (54.9 - 64.6%) -- guaranteed 2HKO
NOTE: Yveltal gets OHKOed by +2 Max Starfall, so if it's AG then you should practically Dynamax it if they Nasty Plot.
Apart from Yveltal, here's another hard counter, Tyranitar:
Tyranitar @ Leftovers
Ability: Sand Stream
EVs: 252 HP / 4 Def / 252 SpD
Careful Nature
- Stealth Rock
- Rock Blast
- Foul Play
- Rest
Sandstorm SpD make it able to hard wall Calyrex-S too, just like Yveltal. Unfortunately, its relying on Rest for recovery which makes it harder to fit. Nevertheless, it's still reliable, just hard to use.
252 SpA Life Orb Calyrex-Shadow Draining Kiss vs. 252 HP / 252+ SpD Tyranitar in Sand: 83-99 (20.5 - 24.5%) -- possible 6HKO after Leftovers recovery
252 SpA Life Orb Calyrex-Shadow Astral Barrage vs. 252 HP / 252+ SpD Tyranitar in Sand: 73-86 (18 - 21.2%) -- possible 7HKO after Leftovers recovery
252 SpA Life Orb Calyrex-Shadow Max Starfall vs. 252 HP / 252+ SpD Tyranitar in Sand: 164-195 (40.5 - 48.2%) -- guaranteed 3HKO after Leftovers recovery
These show the titan's titanic bulk. However, it's mostly relying on Rest which makes it easy to take advantage of.
These are the best counters to it. Apart from those, these deserve a mention, but aren't real counters:
Ho-Oh, Ditto (check), Scarf Kyogre
They can't switch-in to it, but generally force it out.
Hope this helps!