Bakuman。 has a possible in-universe case with Classroom of Truth. At first glance, it is a Deconstructor Fleet story that deconstructs shonen values such as hard work, friendship and so forth, by having the characters trapped in a classroom, only concerned about their own survival, and being forced to admit their selfishness or die. However, Takagi points out that the selfish characters were the first to die, and proposes that it is a roundabout way of suggesting that people must work together.
The Lost Agent arc of Bleach does this to The Power of Friendship. The Dragon Tsukishima uses his Mind Rape powers to turn all of Ichigo's friends and family against him, all while Ichigo has only just started getting some amount of power to protect them. After being helped by Ginjo most of the arc, Ginjo backstaps him and steals his powers, leaving Ichigo powerless against the two as he no longer can protect his friends and they are being used as tools by the antagonists to torment him further. Having always fought to protect people, Ichigo is almost driven to despair by the two, and almost loses hope when he thinks his own father had stabbed him as well. The reconstruction comes from when it turns out the person who stabbed him was Rukia, who restores Ichigo's Soul Reaper powers and arrives with help from Soul Society to save Ichigo and his friends. Essentially the villains weaponized Ichigo's friendships and drove him near to despair, while Rukia and Soul Society showed that the bonds and changes Ichigo had made leading up to this moment still mattered by helping him out.
Cardfight!! Vanguard's first season is this to supernatural card game anime. Psy Qualia allows you to talk to your units, basically letting you draw whatever card you want and see how the game will play out. This is not the first power in this sort of anime that allows you to manipulate the outcome. However, it is shown as bad, not only because it gets you Drunk on the Dark Side, but because at that point, you are not really playing the game anymore. But ultimately, Aichi still thinks of it as The Power of Friendship in relation to his cards, and uses it to defeat Ren, who has the same power but thinks of his units as more disposable.
Dai-Guard is another Humongous Mecha example; it starts out as a deconstruction of the genre heavy on the Surprisingly Realistic Outcome, but then builds back up everything it tore down better than ever. Early in the series, for example, the heroes construct the ever-popular drill arm to deal with an enemy, only to find out that the drill's enormous torque makes it almost impossible to control. But rather than switch to another weapon that is Boring, but Practical, they put their heads together and come up with a giant pile driver arm that works even better than the drill while maintaining the Rule of Cool. It gets taken further later in the series; when the pile driver arm is out of commission, the heroes break out the drill arm again. Only this time it works flawlessly because their extensive piloting experience allows them to compensate for the torque.
Digimon Tamers does work to deconstruct many of the tropes in the previous two Digimon series, such as showing the brutality of owning a Kaiju as a pet and sending ten year olds to save the world, and yet it still revels in The Power of Friendship, Hot-Blooded characters, and most of the antagonists have several shades of gray to them.
Digimon Adventure 02: The Beginning does this with the relationship between Digimon and their partners, as established in Digimon Adventure. Liu realistically acts with horror at the notion that his wish led to the creation of an entire race of sentient beings born into what he describes as "slavery", which is similar to a common criticism aimed to the Mons genre. It takes a talk with Davis to make him understand that it was his relationship with Ukkomon alone that could be described in this way, with the rest of the Digidestined treating their partners as beings worth of respect and love, and not extensions of themselves.
Fullmetal Alchemist uses the Hegelian dialectic from the main page to explain alchemy (it is mentioned that alchemy has three parts when referring to Scar's tattoo (which stops at the 2nd stage): identification, deconstruction, reconstruction). It does this to the plot too, identifying the basic idea of Equivalent Exchange (to which it is the Trope Namer), deconstructing it (The Gate cheated, taking all of Alphonse and taking an arm and a leg from Edward, to give a false revival), and reconstructing it (the real exchange is something different, and comes both from Edward's choice, and Winry's comment to Edward at the end). Both have Equivalent Exchange disputed in rapid succession with providing a better solution, in addition to the gradual deconstruction and reconstruction process provided by the story.
Kaiju Girls: The early episodes are a deconstruction of the Magical Girl Warrior genre. The public is fully aware of them and GIRLS is an organization founded to help them. The Soulrizer is such a mundane (but expensive) device that it is possible to buy a replacement should they break it. Since the world is at peace, seniors in GIRLS have to play Professional Wrestling instead of beating up villains, and newbies get boring tasks like handing out flyers. The reconstruction kicks-in with a berserk kaiju girl, and episode 8 reveals the antagonist organization, Shadows.
Kill la Kill starts off as a clear Affectionate Parody of both hot-blooded shonen and magical girl anime, hanging lampshades on all of the well-worn tropes and generally maintaining its sense of humor above all else. Then Nui reveals that she killed Ryuko's father and starts screwing her over in every conceivable way, and the story becomes more fast-paced and serious, bringing back all of the tropes it lightly mocked and clearly showing why these stories are so beloved.
Most Macross series will do this for the popular anime tropes of their day.
The original Super Dimension Fortress Macross deconstructed the whole "one ship against the world" setup popularized by Space Battleship Yamato showing that an enemy fleet would have to be holding back (as the Zentradi fleet was) for this to work while eventually showing what happens when they do stop holding back. But then they do show how the power of love and understanding can still win the day by giving the lone ship powerful allies.
Macross 7 shows how annoying a typical Hot-Blooded mecha anime hero can be. Then demonstrates how that hot blooded determination can win the day when Basara continues to sing even faced against overwhelming odds, which wins the day.
Macross Frontier deconstructed the Idol Singer aspect by showing how they are mostly "fabricated pop idols" with no substance beyond that, and how they can be discarded at any moment. But then, Sheryl refuses to be discarded and manages to regain her status—and ultimately assists in punishing the agent who tried to discard her, thus truly becoming an Idol Singer.
Nadesico also delves into the Super Robot side of things as well. Many of the moral actions and choices made in the series do not have clear cut results or justifications, and many of the events are contrasted against the Super Robot Show Within a ShowGekiganger. Plus, the only pilot on Nadesico that fits the Super Robot archetype gets shot and killed early in the series, rather than getting the heroic death in battle he was hoping for.
Medaka Box readily flip-flops between being a standard Shonen Jump fighting series and a deconstruction of the same. Initially Medaka is portrayed as a practically perfect All-Loving Hero, but then it's shown despite having seemingly limitless abilities, she has a very hard time relating to or even understanding other people, and that having no purpose in life beyond "help everyone I meet" is dangerously unhealthy. By the end of the series, her kindness towards others has earned her the love of everyone in the school, and those limitless abilities let her save the Earth after her evil uncle tried to drop the Moon on it.
My Hero Academia, being a shonen manga, deconstructs many standard tropes in the genre, to the point of having its own page of deconstructed tropes. However, it ultimately is a celebration of the shonen genre, ultimately reconstructing said tropes (or at least some of them) with a more nuanced take.
Negima! Magister Negi Magi briefly deconstructs the concept of "side characters", showing the kinds of inferiority complexes that can result from people realizing their status. It later reconstructs it by pointing out that even if a person is not in the limelight all the time, their actions can still have a profound effect on the "main characters".
Onani Master Kurosawa: This is done with Because You Were Nice to Me. The characters that fall in love for this reason show that that’s a dangerous overreaction, and said nice person is a False Soulmate (said cases being Kurosawa falling for Takigawa and Kitahara for Nagaoka)... however, it actually is shown to be a good reason to be friends, since those same people prove to be there for A Friend in Need.
The main character is an Invincible Hero whose lack of challenges leaves him completely disillusioned with life. On top of that, his literally unbelievable feats of strength lead the general public to decry him as a fraud. Nonetheless he still keeps on being a hero, because it is what he wants to do, public opinion be damned, and the people who know him personally respect him a great deal for it.
The Hero Association is a send-up of superhero organisations; the higher-ups are affluent morons, many heroes are more interested in their rankings than doing anything heroic (to the point of forming cliques and bullying lower-ranked members), the S-class heroes are dysfunctional at best, and the C-List Fodder is not only severely outclassed by any actual threat, they also have to meet weekly quotas or they lose their membership. And yet it is also a powerful force for good: when a threat that can defeat even S-class heroes emerges, several heroes from across the board rise up to fight it. They stand absolutely no chance, yet by keeping the Monster of the Week occupied they buy enough time for Saitama to arrive and kill it before anybody dies. As Saitama puts it:
"If the heroes run and hide, who will stay and fight?"
Much of the Indigo saga, and especially the first episode, deconstruct the Pokemon journey, showing all the dangers that a less than brilliant 10-year-old kid would get himself into traveling the world unsupervised. Ash nearly gets himself killed on the very first day, and his immaturity and ego blinds him to how he's barely managing his way through the region. However, it's reconstructed through the many friendships that help guide him along the way, proving that while the Pokemon world can be dangerous and even heartbreaking, one can still survive and better themselves in the future.
The first episode starts off as a deconstruction of the whole Pokémon experience, with Ash having to deal with an uncooperative Pikachu and nearly getting killed by wild Pokémon on his first day. Though it seems that his dream To Be a Master is merely a childish fantasy doomed to fail, the episode changes tone when Ash and Pikachu are finally cornered by the Spearow flock. From that point on, the Pokémon journey is reconstructed when Ash decides to selflessly protect Pikachu at the risk of his own life and Pikachu finally returns the favor. It ends on an optimistic and hopeful note for these newly forged friends
The Diamond and Pearl saga spends a heavy section of its run deconstructing The Power of Friendship through Ash's rivalry with Paul. Ash finds himself unable to invoke Underdogs Always Win against a competent opponent obsessed with strength, and his empathy toward his Pokemon frequently serves as his downfall, as he is unable to admit when they just can't win. But after Paul hands him his worst loss ever at Lake Acuity, it finally begins to be reconstructed; Ash swallows his pride and admits that Paul has a point about his training philosophy, and works to find a balance between the two extremes. He learns how to use his bonds to enhance his strategy, not become his strategy, and it pays off when he finally defeats Paul in the Sinnoh League.
Similar to the games, Guzma from the Sun and Moon series deconstructs Always Second Best, becoming a bitter Dirty Coward who preys on weak Trainers and runs away from anyone he might lose to. The members of Team Skull are bounded together by failure, misfits and outcasts too weak to make it on their own. It's reconstructed as his League battle with Ash teaches him to truly face his battles head-on, regardless of the result, and to reflect upon his shortcomings while also recognizing his accomplishments. Not only that, but he realizes Team Skull has given a home and a sense of family to people who were convinced they were losers. He ultimately decides not to disband the team like he did in the games, convinced by his followers that being rougher around the edges doesn't make him a bad leader.
Puella Magi Madoka Magica. Specifically, this series deconstructs the "Power of the Heart" often used in Magical Girl anime. The show does this by drawing attention to the fact that when the characters get to Make a Wish in exchange for assuming the duty of magical girls, these wishes usually have an underlying motive, and their purpose is never as pure and noble as many shows often assume it would be (these are young girls after all). Tragedy ensues not because these wishes had a selfish motive, however: rather, because they were simply badly thought out and the characters were unable to accept their outcome. While initially it seems like An Aesop about the futility of a Deal with the Devil, the ending, however, reconstructs the wish as an embodiment of hope by demonstrating that a wish made for all the right reasons, that benefits many people including the one who made it, essentially becomes the most powerful force to ever exist. It rewrites the laws of reality and recreates the world without the hopeless fate Magical Girls had been previously forced into, even if it, too, comes with a caveat. There is also a decon-recon of the Set Right What Once Went Wrong plot; Homura has tried and failed to find a good ending so many times that it has moved her from the most naive member of the team to a cold-blooded killer, and the repeated failures are gradually eroding her will. However, the sheer karmic buildup this creates is what allows Madoka to win in the end.
Re:Zero is one of the typical NEET protagonist found in Trapped in Another World type stories. Showing first what would happen if a NEET from our world actually wound up trapped in a strange world filled with powerful people and gained a special power, then later showing what it would realistically take for that person to become a hero in this scenario. Because Subaru is weak and unskilled he gets killed very early on and comes back to life only because of his special power (which doesn't lend itself to combat). After going through several cycles of this he starts exhibiting signs of PTSD from all the trauma. In addition, his lack of social skills ends up causing serious problems for himself and Emilia later in the story, prompting a self-inflicted "The Reason You Suck" Speech where he acknowledges all of his failings and how powerless and useless he is. He gradually becomes a hero in his own right by learning from his mistakes, relying on his wits, using the information he gains through each cycle to his advantage, and relying on people that are stronger than him to make it out of battles alive.
Even before TTGL the studio started the era of reconstruction with DieBuster, a direct sequel to Gunbuster that went back to the idealistic roots of the super robot genre.
Gurren Lagann does this itself, with the first eight episodes playing out like an Affectionate Parody of the Super Robot Genre tropes. It does not take itself seriously until Kamina dies, when it deals with the emotional side of the show in a more serious way, while simultaneously celebrating the tropes it mocked in the first place. One can see the history of the genre this way: The first arc is based on 80s Super Robot anime, when the genre was played straight. The second arc is based on the 90s, when it became popular to deconstruct the Super Robot Genre and Real Robot shows were in fashion. The final arc is based on 00s mecha anime, when Super Robot shows got a resurgence in popularity.
It is subtle in Neon Genesis Evangelion, but it is there as well—oh boy is it deconstructed, but the Reconstruction is presented in full postmodernism. Shinji gets over his breakdown, Rei stands up to Gendo, and Asuka finds enough worth to return to life after Instrumentality.
Takopi's Original Sin: The entire story is a deconstruction of Doraemon-style "magical buddy" wish-fulfillment stories, with Takopi's inventions often making Shizuka's situation much worse. Takopi can barely understand humans and has no idea how we really think, so his simplistic, short-term fixes to the problems the three main characters face just end up causing more problems in the future. Before he lost his memories, he also adopted the idea of killing Shizuka to make Marina happy scarily quickly, which shows just how dangerous his shallow worldview really is. That being said, Takopi really does want to help, and he eventually fixes the situation by sacrificing his own life.
Tiger & Bunny first appears to be a Superhero Deconstruction where superhero work has been incredibly commercialized, heroes are in it for the fame and money, the interests of corporate sponsors rule, and ideals of saving people for its own sake has all but disappeared... Until it is clear that, for all the glitz, most of the superheroes are still goodhearted, effective individuals doing what they do because it is right rather than because they get paid for it.
Wake Up, Girls! show isn't afraid to explore the shady side of the Idol Singer industry and the difficulties idols face, but then shows that pursuing one's dreams is ultimately worthwhile despite that.
Yu-Gi-Oh! 5Ds: The series finale pulls this trope on True Companions. By the end of the series, all the members (minus Yusei and Jack) have received opportunities on where to take their lives now that the world is safe, but they’re hesitant to follow up on them as doing so would require them to split up. Jack calls his teammates out on this, saying that by hesitating, they’re choosing not to embrace their full potential as individuals. In other words, their strong bond has become a hindrance rather than a strength. In the end, however, while they do decide to go their separate ways, they resolve to remain True Companions, acknowledging that they can remain connected to one another even if they’re apart.
The premise is clearly a satire of the idol industry, with its long work hours, repetitive content, mental and physical stress, and a lifestyle very difficult to adapt into. This translates into the main characters being zombies, which is about as on-the-nose as anyone can get with metaphors. That being said, the anime also shows that the idol industry can be a place of genuine fulfillment for everyone involved, as long as everyone—from the fans, to the producers, to the idols themselves—remains respectful of one another.
The anime has pointed things to say about the idol industry's concern with having its stars maintain a public image of "purity", firstly by having its idols be corpses, which are about as impure as you can get, then by forcing them to hide the truth about themselves lest they risk alienation. However, it also allows the anime to make a stand for inclusion with Yugiri and Lily, neither of whom would normally be accepted as idols by the industry—the former having been a High-Class Call Girl, the latter a transgender girl—but who are valued bandmates to the other members of Franchouchou, and whom Kotaro recruited anyways despite their background.
Episode 8 shows how the entertainment industry can wreck a performer's life, overstressing them and ruining their relationships, but also how it can be a source of support for them and a way to find catharsis.
, then by forcing them to hide the truth about themselves lest they risk alienation. However, it also allows the anime to make a stand for inclusion with Yugiri and Lily, neither of whom would normally be accepted as idols by the industry—the former having been a High-Class Call Girl, the latter a transgender girl—but who are valued bandmates to the other members of Franchouchou, and whom Kotaro recruited anyways despite their background.