There are many anime series out there where the side characters stole the show so much that viewers considered them to be the story's actual protagonists. The same happened for these series but in a more literal sense.
Whether it was because of a plot twist or their actions drastically changing the story's course, these side characters graduated from the background and into the spotlight, all but overtaking the designated protagonists as the anime's heroes.
WARNING: Spoilers ahead.
10 Baccano! — Isaac Dian & Miria Harvent Were The Timelines' One Constant
With its gargantuan cast spread across history, Baccano! confused viewers and characters with its seeming lack of a focal hero. If anyone were to guess who the protagonist was, it'd usually be the up-and-coming mafiosi Firo Prochainezo. As much as Firo fit the bland protagonist mold, he was barely the star of his own arc.
The true stars of the historical Baccano! were Isaac and Miria, the goofball thieves and comic reliefs who inexplicably bumbled their way into everything from gang wars to the immortals' feud. Minus the 1700s-era prologue, Isaac and Miria were key figures in the anime's major events, as their eccentric brand of heroism saved the day on more than one occasion.
9 Durarara!! — Celty Sturluson Was Ikebukuro's True Naïve Newcomer
Durarara!! opened with the high schooler Mikado Ryuugamine providing the narration, implying that his experiences as a newcomer in the shady paradise of Ikebukuro would be the sprawling anime's main thread. In truth, Mikado was more experienced in the underground than he let on, since he was the founder of The Dollars gang.
The anime's true naive audience avatar was Celty, the Dullahan-turned-courier who had a key role in the city's many crises. While Mikado appeared only when The Dollars did, Celty was all over the city and drove the story forward. Durarara!! even climaxed with her reclaiming her lost identity and memories. Meanwhile, Mikado's angsts were resolved much earlier.
8 A Certain Magical Index — Mikoto Misaka Became The Face Of The Franchise
A Certain Magical Index focuses on the adventures of Toma Kamijo and Index across Academy City, a citywide school populated by eccentric characters and espers like the Level 5 Electromaster, Mikoto Misaka. To newcomers, Mikoto was Toma's most obvious tsundere love interest and a recurring character, but to everyone else, she's the franchise's star.
Mikoto started out as a side character in Index, but she became so popular that she got her own spin-off, A Certain Scientific Railgun, which then overshadowed everything else. Since then, Mikoto became the franchise's de facto protagonist, while Toma was relegated to a more supporting role, even though his series continues to this day.
7 The Melancholy Of Haruhi Suzumiya — Yuki Nagato Was The Protagonist Of An Another Reality
For most of the anime, Yuki kept to herself in the corner of the SOS Brigade's headquarters. At times, Kyon even joked that she was a part of the room's furniture. Both Kyon and the audience's perceptions changed during the finale movie The Disappearance Of Haruhi Suzumiya, where Yuki usurped Haruhi's place as the focal character to change reality.
Though this world was temporary, it expanded into The Disappearance Of Nagato Yuki-Chan, where Yuki overtook Kyon's role as the protagonist of a school life anime. Here, Haruhi studied in another school and only occasionally dropped by the Literature Club, this reality's version of the SOS Brigade of which Yuki was president.
6 Bokurano — Jun Ushiro Saw The Game To Its Bitter End
When 15 unassuming children were chosen by a higher power to defend Earth by piloting the giant mecha Zearth, Takashi Waku took charge and rallied his friends to their newfound mission. The kids put their trust in Waku, and he even volunteered to operate Zearth in their first fight. But then he died in the anime's second episode.
The horrifying truth was that whoever piloted Zearth died after the fight, whether or not they won. As the group dwindled, the anime gradually focused on the Ushiro siblings, especially the abusive brother Jun. Near the end, Jun realized how horrible he was to Kana and others, which motivated him to pilot Zearth in her place and die atoning for his sins.
5 Tengen Toppa Gurren Lagann — Simon Took Up His Dead Brother's Mantle
At first glance, Tengen Toppa Gurren Lagann was as empowering as an action-packed anime should be. The anime was led by Kamina, the undisputed hero who inspired both the subterranean humans and viewers to fight for their freedom. Beside him were his friends, his love interest, Yoko, and his constantly underestimated younger brother, Simon.
During the opening episodes, it seemed as if he would lead and finish the fight, but then Kamina died before the first arc even ended. Simon then took Kamina's place, revealing the anime to be his wartime coming-of-age story. Over the remaining episodes' course, Simon stepped out of his brother's shadow to become his own leader and person.
4 Higurashi: When They Cry — Rika Furude & Satoko Hojo Were More Than Just Potential Love Interests
Whenever Higurashi reset the massacre of June 1983, someone from Keiichi's friend group would be the new focal character. Despite this revolving door, many assumed that Keiichi Maebara was the default main character. While Keiichi was an important constant, he only had a supporting role in Rika's (left) story, the true protagonist and a part of his harem.
Simply put, the time loops came to be because of Rika's death at Takano Miyo's hands. At some point, Rika became aware of her reincarnations and has been trying to break the cycle. This was then flipped again in Gou, where Rika's scorned childhood friend and (possible) lover Satoko (right) was revealed to be the sequel's tragic overall villain and protagonist.
3 Re:Creators — The Anime Was Meteora Osterreich's Story To Tell
Despite having a massive ensemble cast, it seemed pretty obvious to viewers that the regular high schooler Sota Mizuhino and the light novel/anime warrior Selesia Upitiria were the main characters. Both guesses were wrong not only because Sota was slowly pushed to a supporting role and Selesia died but because Meteora took control of the narrative.
Meteora was a JRPG's expositional NPC and, true to her nature, she kept tabs of the Creations' collision with reality as it occurred. Her comically biased narration in the meta recap episode actually foreshadowed her status as the true protagonist, which was cemented by her novel, "Re:Creators," that she wrote after she chose to stay in the human world.
2 Puella Magi Madoka Magica — The Anime Was Homura Akemi's Time Loop
Even if her name was in the title, Madoka Kaname was not Puella Magi Madoka Magica's protagonist. It could be argued that Sayaka Miki was the typical magical heroine, while Madoka was her non-magical best friend. The truth is that the quiet anti-hero Homura was the true protagonist, because the anime could only happen thanks to her actions.
Madoka's big twist was that it was the nth iteration of a time loop that Homura trapped reality in. Homura did this as part of her desperate fight to save Madoka from dying or worse, and this struggle was the anime's true crux. At most, Madoka was a sentient Deus Ex Machina who Homura and the Incubators fought tooth and nail for.
1 SSSS.Gridman — Akane Shinjo Needed To Be Saved From Her Inner Darkness
Like any good tokusatsu story, the animated sequel to Gridman The Hyper Agent focused on an unassuming kid (namely Yuta Hibiki) inheriting the power of Gridman and using it for good. While Yuta and Gridman played the part of the infallible hero to perfection, the anime wasn't their origin story but a character study of the antagonist, Akane.
In truth, Yuta, Gridman, and their allies were little more than side characters and stepping stones towards Akane's self-realization. This explains why Yuta and Gridman were static paragons, while Akane got the most dynamic character development. The finale focused mainly on Akane, while Gridman returned to his dimension after saving her.