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Zekrom is a very good check to Ho-Oh as Zekrom resists the fire- and flying-STAB from Ho-Oh and it has options to heal itself up with Roost and can strike back with its Bolt Strike STAB.
The only move Zekrom has to fear is the switch into Earthquake as it can still pose a threat towards Zekrom, but in overall Zekrom has measures to deal with Ho-Oh during a battle.
Calcs:
4 Atk Teravolt Zekrom Bolt Strike vs. 4 HP / 0 Def Ho-Oh: 438-516 (123.7 - 145.7%) -- guaranteed OHKO
4 Atk Teravolt Zekrom Dragon Tail vs. 4 HP / 0 Def Ho-Oh: 102-120 (28.8 - 33.8%) -- guaranteed 2HKO after Stealth Rock
252+ Atk Choice Band Ho-Oh Sacred Fire vs. 252 HP / 252+ Def Zekrom: 85-101 (21 - 25%) -- possible 5HKO after Stealth Rock and Leftovers recovery
252+ Atk Choice Band Ho-Oh Brave Bird vs. 252 HP / 252+ Def Zekrom: 102-121 (25.2 - 29.9%) -- 94.3% chance to 4HKO after Stealth Rock and Leftovers recovery
252+ Atk Choice Band Ho-Oh Earthquake vs. 252 HP / 252+ Def Zekrom: 228-270 (56.4 - 66.8%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
SR Arceus-Water as a soft counter
Arceus-Water @ Splash Plate
Ability: Multitype
EVs: 252 HP / 16 Def / 144 SpA / 96 Spe
Timid Nature
- Stealth Rock
- Judgment
- Ice Beam
- Recover
Stealth Rock Arceus-Water can outspeed and 2HKO Choice Band Ho-Oh while easily taking a Sacred Fire or Earthquake. Although it doesn't appreciate getting hit by Toxic, being poisoned won't let Ho-Oh win the matchup unless it clicks Brave Bird, and Sacred Fire can even make it so that Toxic won't work on it. Also, even if Brave Bird does a great amount of damage, Arceus-Water can still win the 1v1 if it switches on it, as Brave Bird's recoil makes Judgment a roll for a OHKO, and any chip damage prior will make it guaranteed. Seeing that it forces Ho-Oh out too, it can use that turn to use Recover to mitigate the damage taken or use Stealth Rock, which not only brings utility to the team, but also makes Judgment a guaranteed OHKO, essentially nullifies Regenerator and make it so it can't click Brave Bird freely, as it will take too much damage.
144 SpA Splash Plate Arceus-Water Judgment vs. 4 HP / 0 SpD Ho-Oh: 236-278 (66.6 - 78.5%) -- guaranteed 2HKO
252+ Atk Choice Band Ho-Oh Brave Bird vs. 252 HP / 16 Def Arceus-Water: 271-321 (61 - 72.2%) -- guaranteed 2HKO (25.2 - 29.9% recoil damage)
252+ Atk Choice Band Ho-Oh Sacred Fire vs. 252 HP / 16 Def Arceus-Water: 114-134 (25.6 - 30.1%) -- guaranteed 4HKO
252+ Atk Choice Band Ho-Oh Earthquake vs. 252 HP / 16 Def Arceus-Water: 152-179 (34.2 - 40.3%) -- guaranteed 3HKO
Zygarde @ Leftovers
Ability: Power Construct
EVs: 252 HP / 252 Def / 4 SpD
Impish Nature
- Rest
- Glare / Sleep Talk
- Thousand Arrows
- Coil
Defensive Zygarde-Complete can easily stomach any of Ho-Oh attacks - it is a counter due to being the only mon in USM that is capable of avoid being 3HKO by its strongest STAB Brave Bird as long as you don't get crit and is not vulnerable to status thanks to Rest. In response Ho-Oh will receive a large sum of recoil damage due to Zygarde’s colossal HP. Once it withstood Ho-Oh's attacks, it can set up Coil making Ho-Oh’s situation even more helpless and proceed to power through Ho-Oh. Calcs:
252+ Atk Choice Band Ho-Oh Brave Bird vs. 252 HP / 252+ Def Zygarde-Complete: 204-240 (32 - 37.7%) -- 0.2% chance to 3HKO after Leftovers recovery
Salamence @ Salamencite
Ability: Intimidate
EVs: 248 HP / 136 Def / 124 Spe
Impish Nature
- Body Slam
- Defog
- Roost
- Refresh
Thanks to Refresh M-Salamence doesn't need to worry about Toxic. Body Slam comes with a decent chance to inflict paralysis on Ho-Oh or pokemon looking to switch into Salamence. Nominated as a check.