The characters of the Persona series all have unique powers and abilities across their independent games and iterations. Some games portray characters that can fight and defeat literal gods and incarnations of desires, while some struggle against henchmen type enemies. Figuring out who is the most powerful is pretty simple though, since the games give fans an overall context of what is strong and what isn't.
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For example, every protagonist has the wild card ability which allows them to wield multiple personas. This means they can use the persona born from their own souls, or a literal angel from the heavens if they choose. After that, it all comes down to their unique abilities.
10 Makoto Yuki (P3)
The protagonist of Persona 3 is almost without a doubt the strongest persona wielder in the entire series under normal conditions. He inherits the Universe arcana which allows him to seal Nyx, a world threatening god of death. This means his power is on par with characters from the Velvet Room who have also been shown to take down humanity's negative emotions that incarnate themselves as gods.
Since Yuuki is the only character to get the Universe arcana, it's unclear that the limits of his power actually are. When he obtains it, even Igor, the master of the Velvet Room, says he doesn't know how strong the arcana truly is. It's safe to assume there're more abilities sealed behind the arcana since it's mentioned in other games but only bestowed to Yuuki.
9 Maki Sonomura (P1)
Maki is an interesting case in the Persona universe because her true power is only activated within very specific circumstances. Maki's power comes from the fact that she is the "ideal" version of herself that exists in a parallel universe, which was birthed from her own thoughts. After defeating other, more evil versions of herself, Maki gains control of her parallel universe and essentially can do whatever she wants in it.
Maki may not be as strong as other characters from the Persona universe normally, but her powers are nothing to be laughed at. Fans speculate that there're probably only 1 or 2 threats in the universe that could contest Maki at full power, and none of them are persona users.
8 Tatsuya Suou (P2)
Tatsuya is the second strongest protagonist of the Persona series because of the interesting abilities be obtains at the end of Persona Eternal Punishment. Tatsuya has the power to stop time with his persona, which is unlike any other ability in the Persona universe that persona users can do. This ability alone puts him above most and make him unique as a protagonist.
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On top of the ability to stop time, Tatsuya can also end the entire universe if he decided to. This power is not exactly his own, but he holds the key to it. Because of the resolution of his story, he had to give up the bonds he created with his friends to save the world. If memories of him return to his friends, the whole universe would cease to exist, causing a stalemate with whatever opponent he's facing.
7 Ren Amamiya (P5)
Ren is the protagonist of Persona 5 who, like his predecessors, takes out a god of some sort as his final boss. Ren has the wild card ability which lets him wield multiple personas, as well as negotiate with shadows. He has the most communication with any shadows of any protagonist which doesn't necessarily equal strength, but it means he could gather very strong personas to use in battle.
This protagonist also evokes his persona in a unique way when compared to those of other games. In Persona 5, the first appearance of his persona seems to cause great pain but is easy to summon after that without much effort. Being able to summon a persona without much effort or evoker is a sign of strength within persona users, so it might be a good indication of his true potential.
6 Junpei Iori (P3)
Junpei Iori is a stronger persona user than most because of his special fusion with Chidori in Persona 3. Because of this fusion, Junpei retains his own abilities while obtaining the special abilities of Chidori, who was an exceptional persona user herself. Medea, Chidori's persona, was able to give life, use telepathic abilities, and had other small specific powers.
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Using the Spring of Life ability from Medea, Junpei essentially gains a second life that would heal any wound and save him before death. Junpei's strength combined with this healing factor make for an unstoppable powerhouse unlike any other persona user in the series.
5 Yu Narukami (P4)
Out of all the Persona protagonists, Yu Narukami is probably the weakest. Even though he is the weakest protagonist, he is still an insanely strong persona user in his own right. He has the wild card ability that allows him to wield multiple personas, and he takes out Izanami in the true ending of Persona 4.
The issue with Izanami's defeat is that Yu Narukami didn't do it on his own. He relied on the strength of his bonds, and the power of friendship (no joke) to take out the final boss of the game. It's hard to say what the implications of this event really are, or what they mean for assesing his strength, but at least fans know that the power of anime can get them pretty far.
4 Tohru Adachi (P4)
Adachi is another interesting case since he is technically a wild card user himself like the protagonists of each game, who also has his own special powers. He calls forth his persona without an evoker or normal means like in Persona 4, which is reminiscent of early persona users.
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Adachi has the same persona as Yu Narukami, and the wild card ability which puts them both on even ground. He can also talk to shadows and command them within his TV world without becoming a shadow which is an interesting ability that indicates that he has the wild card. Other than that, his strength comes from his own negative emotions instead of positive ones like the protagonist, so it could be said that he is even stronger than his counterpart.
3 Velvet Room Members
The strength of characters like Elizabeth and Theodore is hard to truly measure because they're not human, and their powers aren't shown in battle too often. What they have shown, is the ability to take on any party from the games, crazy abilities specific to them, and huge bursts of power like when Elizabeth took down Erebus in one hit.
The Erebus incident is telling because Erebus is the manifestation of all of humanity's grief and sorrow, making it a powerful demon in the world of Persona. Elizabeth disposing of it in one hit means that other world threatening beings would probably be no match for her outstanding power.
2 Goro Akechi
Another wild card user who is able to use multiple personas, like Robin Hood and Loki. Not only is Akechi able to use multiple personas, it's also implied in Persona 5 that he was able to clear the same palaces as the Phantom Thieves, all by himself. The Phantom Thieves had 5 or 6 members at the time with reconnaissance and could change their squad depending on the situation, so tackling a palace solo is obviously no small feat.
Aside from his persona and physical strength, Akechi also had the ability to make people around him go berserk. All these special abilities and powers in tandem made him a bigger threat than some protagonists of the series, even after they awakened their personas or got their big end game buff.
1 Aigis (P3)
Aigis is the most unique persona user of the universe and Persona 3. Aigis inherits her wild card from the protagonist of persona 3, and is strangely adept at using it. She can't use fusion abilities like other protagonists, but she has access to the velvet room and multiple personas.
In addition to these special abilities, she's a literal killing machine. Aigis is equipped with machine guns, rocket launchers, blades and an unknown array of other weapons. In terms of straight firepower, Aigis is the strongest persona user who will not lose in a physical fight. Her hard exterior and weapons are also helpful for any situation where she can't use a persona and has to defend herself.
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