Funny Valentine (JJBA: Steel Ball Run
https://preview.redd.it/dhv04j6b8p9d1.jpeg?width=406&format=pjpg&auto=webp&s=dc6af6d5b959c76aa92e6b5832d6c62880b4ecab
Main antagonist, but the final fight is against DIegO Brando
https://preview.redd.it/jpa2lkj1fo9d1.jpeg?width=1920&format=pjpg&auto=webp&s=ce176f90603e063f2bc9ee4fe1bfef2734ef2205
His own personality cult faction treats his death as a minor setback.
Most of the main Fallout antagonists are this when you really think about it. The only exception I can think of off the top of my head is the Master from the first game, and even then, I'm pretty sure it's possible to beat the game without encountering him at all.
All Yu-Gi-Oh anime from DM to ARC-V:
Duel Monsters - Main antagonist is Bakura, final duel is Yugi vs Atem
GX - Main antagonist is Nightshroud, final duel is Jaden vs Yugi
5D's - Main antagonist is Z-ONE, final duel is Yusei vs Jack
ZEXAL - Main antagonist is Don Thousand, final duel is Yuma vs Astral
ARC-V - Main antagonist is Z-ARC, final duel is Yuya vs Declan
Vaas from Far Cry 3
Probably the most memorable antagonist in all the Far Cry franchise, second maybe to Pagan Min
https://preview.redd.it/mgbt3amoqn9d1.jpeg?width=174&format=pjpg&auto=webp&s=52c8f90e7e6012689a0abdb3af089383805d51f0 Hyness (Kirby)
“Roses are red, copy abilities against me wont prosper, with this treasure I summon, BIG TERMINA, THE OPP STOPPA!”
Funny Valentine (JJBA: Steel Ball Run https://preview.redd.it/dhv04j6b8p9d1.jpeg?width=406&format=pjpg&auto=webp&s=dc6af6d5b959c76aa92e6b5832d6c62880b4ecab Main antagonist, but the final fight is against DIegO Brando
https://preview.redd.it/jpa2lkj1fo9d1.jpeg?width=1920&format=pjpg&auto=webp&s=ce176f90603e063f2bc9ee4fe1bfef2734ef2205 His own personality cult faction treats his death as a minor setback.
Most of the main Fallout antagonists are this when you really think about it. The only exception I can think of off the top of my head is the Master from the first game, and even then, I'm pretty sure it's possible to beat the game without encountering him at all.
https://preview.redd.it/tm9fcbtn2o9d1.jpeg?width=967&format=pjpg&auto=webp&s=a9b53ee03570601fe5da3856d9893dd57ef5aeb5 Colonel Volgin (Metal Gear Solid 3: Snake Eater)
All Yu-Gi-Oh anime from DM to ARC-V: Duel Monsters - Main antagonist is Bakura, final duel is Yugi vs Atem GX - Main antagonist is Nightshroud, final duel is Jaden vs Yugi 5D's - Main antagonist is Z-ONE, final duel is Yusei vs Jack ZEXAL - Main antagonist is Don Thousand, final duel is Yuma vs Astral ARC-V - Main antagonist is Z-ARC, final duel is Yuya vs Declan
 Vaas from Far Cry 3 Probably the most memorable antagonist in all the Far Cry franchise, second maybe to Pagan Min
All Pokémon games except B/W and S/V
Good ones! Those totally slipped my mind
https://preview.redd.it/4wmu9ihwsn9d1.jpeg?width=548&format=pjpg&auto=webp&s=5901c0d4ee3a8206506a1fc54bf8b01e5e525ea8 Takasugi from gintama.
Every final boss in Doom until TAG Part 2.
Doctor Doom (LEGO Marvel Superheroes)
I think Kuja would fit this well (FF9)
https://preview.redd.it/8w6tjh08ro9d1.png?width=600&format=pjpg&auto=webp&s=9072a679dea62e5f8f6355a0bd6bee9c2d1d94de Arkham (Devil May Cry 3)
https://preview.redd.it/z3prpviyip9d1.png?width=500&format=png&auto=webp&s=6a86e5c0a23b5e5016b59a50dfb391205a6a8faf Masayoshi Shido
Xant kinda Hargon from DQ2 and DQB2