Plenty of anime like Attack on Titan have a tendency to blur the line between villain and hero, but in others, the line is very clear cut. Even in shows with distinct villains and heroes, sometimes the paths of those characters cross and they're forced to work together for a common interest.
Rarely do villains get a happy ending in their stories, but moments like these are often a triumph for both the antagonist and protagonist. The best of these scenes almost always show a moment of humanity for the bad guy at some point in the adventure, making it more difficult to root against them.
Frieza In The Tournament of Power
The Tournament of Power arc featured plenty of villains to heroes like Vegeta and Android 17, but it also included someone who remained a villain the entire time: Frieza.
Frieza is evil, but he isn't an inherently destructive being. Everything he does is in the interest of retaining his power and status as ruler. Even his horrific destruction of Planet Vegeta ultimately was just to remove any threats to opposing his grip over his empire. Thus, it stood to reason that Frieza would do anything he could to save his universe by helping Goku defeat Jiren.
Shark and Yuma vs Don Thousand
Shark made a journey from the lovable Yu-Gi-Oh! Joey clone to a terrifying force that opposed Yuma. Even still, the two frequently worked together. First, when Shark fought secondary antagonist Vector. Second, when the two worked together to defeat Don Thousand, a threat to the entire universe.
Shark was never inherently evil like other antagonists that have teamed up with heroes. Shark, ultimately, was just an ally to his true species: the Barians. While the Barians clashed with humanity and the Astral World throughout the final season, it was never in question that Shark would team up with Yuma to save all three worlds.
Aizen and Ichigo Fight Yhwach
Aizen was the cold and calculating main antagonist throughout most of Bleach, but finally, an even greater threat presented itself: Yhwach. Ichigo and co enlisted Aizen's help to take down the foe, and the genius villain eventually ed them on the battlefield.
Aizen ended up playing a crucial part in the battle against the enemy, using his complete hypnosis as team Ichigo's final trump card.
Hisoka Helps Gon In Dodgeball
Hisoka is one of the most beloved villains in anime, and also one of the creepiest. In a fateful game against Razor for one of the most important cards in Greed Island, the antagonist teamed up with Gon and Killua for an intense game of dodgeball that saw the trio barely defeat Razor after a combo move that needed all three fighters to work perfectly in tandem.
Greed Island was another example of Hisoka working together with the protagonists for his own gain, but he was never once set up as a hero in any way during the story. The game helped show Hisoka is a hedonist to the end, as he has continued to be throughout the manga.
Sasuke and Naruto Team Up In The Last Arc
Naruto and Sasuke have a complicated relationship throughout the series, but there's no doubt that Sasuke was a villain in the final arc of Shippuden. Despite this, Sasuke wasn't so blinded by rage that he couldn't see Madara Uchiha (and eventually Kaguya) needed to be defeated.
At the end of the day, the two had one of the most emotional final fights in anime history. But before that, they were once more comrades fighting for the greater good. Just like in the days of the original series.
Magma Assists Senku
Magma and Senku hunting for Tungsten was a pivotal moment for the minor antagonist and protagonist of Dr. Stone. Magma, the powerful meathead, had been against Senku and his science the entire series up until his decision to save Senku in the caves by hurling him safely out of the deep water-filled pit Senku was finding difficulty in treading. Eventually, the water rose to enough of a height for Magma to reach the surface as well, and the two escaped unharmed.
The moment was incredibly important for Magma, and his first real bit of development. Magma learned to appreciate science in this encounter with Senku and finally became a committed warrior for the team after much time as an antagonist.
Grimmjow Heals Ichigo
Grimmjow wasn't exactly the smartest Espada in Bleach, but at the very least he knew what he wanted. Ichigo was completely dead to rights by Ulquiorra's hand, and Grimmjow made the decision to grab Orihime and take her to Ichigo so that she could save his life. Along the way, Grimmjow held off Ulquiorra so that Orihime could work her magic.
Ultimately, Grimmjow just wanted one final fight with Ichigo and would do anything to get it. However, the moment showed Grimmjow's potential to be a valuable ally to Ichigo, despite how the encounter ended.
James and Inkay Save Everyone Against Malamar
When a group of evil Malamar were on a rampage in "Facing the Grand Design!" James and his Inkay, two of the few not paralyzed by the Malamar, were especially clutch, and the combined forces saved the day.
There have been plenty of other times in the series where Team Rocket has assisted Ash and co as well, including saving Ash in "A More Perfect Union" and in Pokémon 3 the Movie: Spell of the Unown.
Nero and Avilio's Last Ride
Arguably the best mafia anime of all time, 91 Days stars the mafia heir Nero Vanetti and familial avenger Avilio. For most of the series, Avilio pretends to be Nero's best friend before ruining life for the Vanettis and disclosing his desire for revenge after his own family's death at the hands of Nero's family.
After their hatred for one another is aired out, the two decide to go for a final ride to see if they can feel something worth living for. The two travel together for days, helping each other along the way until they finally reach the beach. In Avilio's last moments on the beach, Nero discloses that nobody needs to find something to live for and that "you just live."
Askeladd and Thorfinn's Arrangement
After Askeladd killed Thorfinn's father, the young boy swore he would defeat Askeladd in a duel. However, in order to get the right to the duel, Thorfinn first had to prove his worth to Askeladd.
From then on, the entire first season of Vinland Saga followed the adventures of Thorfinn and Askeladd as Thorfinn earned the right to duel Askeladd again and again, only to lose every time they fought. The pair has one of the most fascinating and heart-wrenching relationships in anime, and their partnership never fails to deliver.