In Asatte no Houkou, Karada and Shokou are able to switch back to their original ages when Kotomi gives them a second wishing stone, which she had never previously mentioned or hinted at having. This, of course, didn't happen in the manga.
Ulquiorra reveals that he has a second, more powerful transformation and deals Ichigo a fatal wound. Suddenly, Ichigo's hollow takes over, and turns into a super form that tears Ulquiorra apart. While the hollow had been shown to transform as Ichigo gained power, nothing suggested that it could bring him back from the brink of death.
By the end of the Deicide arc, Aizen had become so powerful that it took several consecutive dei ex machinis to take him down. After Aizen curb-stomped everyone in his way and developed the ability to heal from any wound, Isshin takes Ichigo to teach him a never-before foreshadowed technique that channels all his spiritual into his physical strength, leaving Aizen completely helpless against him. When that's not enough, the Hogyoku spontaneously rejects Aizen, and then it's revealed that Kisuke implanted a special kido into Aizen that would seal him if that exact scenario happened.
Yhwach is so strong that only the most powerful Shinigami, Yamamoto, can match him in battle. Yhwach can place shards of his soul into people, helping them become more powerful. When he reclaims his shard, he absorbs the energy of the person in the process, killing them to empower himself by leaving behind a blood clot made of Stil Silver that makes its way to their hearts. He can draw energy from his minions whenever he wants and he can predict all of his opponents moves before they even know what they're going to do. He can also overcome any other ability if he studies it long enough, negating even successful attacks against him by changing the future. It's made clear by even Mayuri, Yamamoto and the Quincies that Yhwach is basically unkillable. Only when the final battle begins is a way to kill him revealed: Ryuuken forged a secret arrow nine years ago from the Stil Silver that killed his wife; Uryuu learns his power can negate Yhwach's ability to see his future, allowing him to fire Ryuuken's arrow without Yhwach detecting it. The arrow nullifies Yhwach's power for a second, allowing Ichigo to kill Yhwach, whose dying thought is the realisation that Haschwalth disloyally disguised a future vision of his death as a dream so that he would ignore it. Simultaneous to Ichigo's killing blow, Yhwach begins reforming ten years in the future, only for Ichigo's young son to touch his manifesting reiatsu; instantly negating the reformation, he ensures Ichigo's killing blow succeeds.
In Cardcaptor Sakura, The Power of Love proves itself to be quite this trope. At the end of the TV series, Sakura accidentally ends up creating a new nameless Card when her powers react spontaneously to her tears at Syaoran's departure. At first glance it appears to be a Sequel Hook, but fast forward to the end of the Sealed Card movie, where at the last moment, it negates the Void Card's power and combines with it to form the Hope card, protecting Syaoran from losing his love for Sakura and allows it to be captured, restoring everything (and everyone) back to normal. Another example is when Sakura encounters the illusion card, which, on the date of her dead mother's birthday, adopts her form, and thus lures Sakura into falling off a cliff. Before hitting the ground nonetheless a translucid hand (that of her real mom) appears out of nowhere and slows down her fall. And as a backup Deus Ex Machina Yukito just happened to be passing by at that precise moment to come and catch her.
Detective Conan, Conan can do anything at given times from riding a motor boat, a helicopter, and shooting guns with a common excuse of "My dad taught me that in Hawaii". The movies happen to be much more action oriented compared to the cases seen throughout the show where you'll only come across action related content during episodes/arcs related to the Black Organization. The good news though is that the Hawaii excuse is only ever used throughout the non-canon movies so in regards to Gosho Aoyama's manga, this copout doesn't overlap with the source material.
In volume 5 of Daichouhen Doraemon, after a lot of time traveling and reality altering that ends up in them being petrified by a demon, Doraemon and Nobita are very fortuitously saved by Dorami, Doraemon's little sister, almost at the end of the book, even though she doesn't even make the cover, merely because there's a distress signal from a gadget of hers known roughly as "Bug Omen Alarm".
When Frieza is revived and comes to destroy the Earth, everyone is crapping their pants because Goku was "the only one" who had a chance at beating him. Then, out of nowhere, Trunks appears, killing Frieza with a few slashes, then King Cold shortly after. Yes, Frieza was a way of giving the Z Fighters' newest ally his big introduction to set up the Android/Cell sagas, but that doesn't keep him from looking like something out of a fanfic.
In order to beat powerful enemies like Lord Slug and Broly, the Z Fighters transfer their power to Goku, which gives the latter a tremendous boost in strength, more than enough to destroy the enemy in a dominating fashion. Said ability is never elaborated (at least not to that extent) in the main series, where it would have no doubt made some of the biggest fights a lot simpler.
On the subject of the defeats of villains in movies, in Wrath of the Dragon, Goku uses a previously unseen attack called the Dragon Fist to kill the seemlingly unstoppable Hirudegarne.
When Vegeta attempts to wish the earth back and everyone who's died since the day of the tournament. Dende tells Vegeta about the previously established limitation of Porunga: he can only bring back one person at a time. Then suddenly the new Grand Elder tells Dende that after Freeza they upgraded Porunga's powers, so they can bring back more than one person. This one is not quite as bad, as a dragon has had it's power upgraded before, but it's awfully convenient the upgrade happens to be exactly what the protagonists need.
When Goku and Vegeta use the Potara earrings to fuse into Vegito, this is something of a Godzilla ThresholdHeroic Sacrifice, as Potara fusion is permanent. Then, after they deliberately get absorbed by Super Buu, the fusion falls apart, for no adequately explored reason, which is Hand Waved as something about the effects of being in Buu's body. Dragon Ball Superretcons this into the much more sensible explanation that Potara fusion is only permanent if a Kai is involved.
Tenkai Knights the Tenkai Wolf, a creature who'd never been mentioned before (and had the flimsiest foreshadowing ever) suddenly appears and easily defeats the good and evil halves of the Tenkai Dragon before they're fighting inadvertently destroys the planet.
Played straight (and literally) in the last few volumes of Fushigi Yuugi. Taka buys Miaka a pager. Suzaku then ends up taking up residence, essentially, in the pager, so that he can contact his priestess.
Mic Sounders of GaoGaiGar. His Disk P Theme Music Power-Up powers up (and seemingly to a small degree repairs) all of the heroes within earshot (and is also continually used throughout the series). Disk M can disable mechanical systems in only the bad guys (it?s ability to selectively deactivate the bad guys system is in itself somewhat deus ex machina-y). On the much more dangerous side he has his disk x which destroys things at the molecular level, meaning there is literally nothing it cannot destroy and the even more powerful disk F which can produce a Gao Figh Gar armed with the Goldion Hammer to destroy anything in his path. Basically if Mic were to ever receive a major upgrade, much like some of the other mechas receive, then he would render GGG totally obsolete since the only step up from Disk X and F is a disk that completely controls the very fabric of reality.
Somewhat lampshaded in Hellsing where the giant zeppelin of the Magnificent Bastard Major is called the Deus Ex Machina- appropriate seen as how it appears from nowhere to bomb London.
In Initial D, when Takumi battles the Todo School's rally driver with the School's demo car at Happogahara, he is absolutely going to lose until a cat jumps out in front of the Civic just before the final corner. When the driver swerves to miss it, Takumi passes, not seeing the cat because his lights were off.
A major sticking point with fans at the end of Part 3 is Jotaro's spontaneous development of Time Stop in his fight with DIO, which enables Jotaro to fight DIO on more or less equal terms. The only possible foreshadowing of this is DIO's comment that he and Jotaro share a similar type of Stand, but DIO is just as shocked as the reader when Jotaro is able to move during DIO's Time Stop. It's still not as ridiculous as in Part 5 since DIO's vampire stamina allows him to stop time for longer than the human limit of five seconds while Jotaro struggled to move for even two to three seconds, meaning the latter was still at a ridiculous (but not hopeless) disadvantage.
Another one comes at the end of Part 5, when Giorno fights Diavolo. Giorno is pierced by the Requiem Arrow, and his Stand Gold Experience gains the ability to ''negate any action taken by an opponent.'' Stands had been shown to develop new abilities thanks to the arrow before, but that power is ridiculously broken.
Part 2 eventually has the Big Bad Kars becomes immortal, being able to survive being roasted alive in a volcano and being able to curb stomp the good guys. Joseph admits his defeat as the battle is truly hopeless and he's run out of plans... then Kars's finishing move, a Hamon strike that he suddenly gained the ability to use, gets bounced and amplified by the Red Stone of Aja, creating a giant volcanic eruption and along with other things being tossed that launch him into the outer space, where he is ultimately frozen alive and floating around the universe for eternity.
Lampshaded by Joseph; he proclaims to Kars that he had planned it out from the start, even as he privately thinks to himself that it's an amazing stroke of luck that he could never have predicted, purely as one final "Fuck You" to send Kars off the edge of his Sanity Slippage.
Part 2's example is a bit less blatant than others, as (at least in the anime) Joseph can be seen grabbing the Red Stone right as he starts fleeing from Kars. An earlier scene has Lisa Lisa demonstrate the stone's ability to amplify solar energy, implying that the same can be done to Hamon with it. The first antagonist of part 2, Straizo, demonstrates that undead beings can still use hamon, but would normally kill themselves doing so. And the Pillar Men have previously been shown learning new languages within minutes, demonstrating their genius intellect that allows them to learn new things incredibly quickly. This all provides some foreshadowing as to how Kars is eventually taken down (or rather up).
Another example is the end of the Kyoto Arc, where the Negi party was saved from the Big Bad and the Demon God he unsealed by the equally demonic unsealed Evangeline.
Martian Successor Nadesico tap-dances across this trope in the final episode. To get the Black Box out of Mars, a specific link is needed to get it activated. In this case, a kiss. Yurika, however, is more willing to blow the *** thing up as it's the cause of all of their troubles. Akito goes after Yurika and is able to stop her and tells her that he was finally able to watch the final episode of Gekiganger III... and was incredibly dismayed when he found out the final episode had Joe, whose poignant Heroic Sacrifice mirrored the loss of Akito's friend Gai, come Back from the Dead with the original Gekiganger III to save the day. He points out that those things can't happen in real life and we shouldn't expect them. Which is hilarious as he finally kisses her, the teleportation works and, apparently, their first admiral was actually still alive and rejoined the gang.
A borderline case appears in the second season of Mobile Suit Gundam 00: with the forces of Celestial Being about to be defeated, Setsuna, who has been slowly undergoing Innovation (a cornerstone of the show's ongoing Gambit Roulette), finally achieves it. This, in turn, triggers a hidden system of his machine, the Trans-Am Burst, which spread on a much larger scale the effects the machine was already known to have (healing, telepathy, etc). Given that The Chessmaster had already been established to have built-in hidden subroutine in his mobile suit to be triggered as his roulette demanded, and that it's shortly thereafter that a world-wide mind-meld was a key point of said roulette, fan opinion is divided as to how much of a Deus Ex this is, if at all, and if so, whether it qualifies as an old school Greco-Roman Deus Ex, or the Fridge Brilliance variety.
And, before we continue to the next subject matter, this Deus Ex Machina in question also somehow cured Louise Halevy of her particle poisioning, as she was about ready to succumb to her genetic breakdown. Depending on your viewpoint, this was the saving grace Louise needed after a hard couple of years, or you looked at the show basically giving her a free pass for the crap she did to thousands of innocents, her friends, her boyfriend, and even that person who was responsible for ruining her life, if you want to add her to the equation.
Gundam 00 practically spammed Deus Ex Machina from beginning to end. Almost every time Celestial Being came even remotely close to defeat, A.) one or more of the Gundam Meisters would reveal a weapon or a feature that was previously not shown nor hinted at before, such as the case of the Nadleeh and later its Trial System or B.) be saved by the intervention of an outside force like the Thrones or C.) one of old man Aeolia's little hidden features (i.e. Trans Am) would trigger, essentially, a more grandiose version of A. This was especially insulting for their opposition, who would make painfully detailed strategies that exploited the Gundams' (known) weaknesses and would have otherwise been successful until Deus Ex Machina kicked in. And as with the first example, it is extremely hazy to wether it is regular old Deus ex or a case of Fridge Brilliance catching up.
Sasuke pulls off a No One Could Survive That! by summoning, mind-controlling, and teleporting a massive snake when he's completely out of chakra. Said technique is difficult because of the huge amount of chakra required. He pulled this all off in the time it took for an explosion that would completely level a city to reach him. After the explosion had already started. When it started just a few feet from him. Great Snake Escape, indeed.
After spending the last thirty chapters wreaking havoc Nagato pulls a case of Redemption Equals Death and a device that was only shown to be able to repair corpses to bring back everyone that he had killed since entering the village.
During his assault on the Kage Summit, Sasuke nearly died from chakra exhaustion, having been spamming the crap out of high level techs with his new Mangekyo Sharingan. And then, out of nowhere, Zetsu, who had previously shown up to alert the Kages to Sasuke's presence and gotten killed for his efforts, reveals that he managed to use a time release jutsu in the split second before the Raikage snapped his neck that sucks all the chakra out of everyone in the room and gives it to Sasuke.
Itachi Uchiha suddenly uses Izanami. Izanami is only useful against Izanagi users and Kabuto or those like him, whom the user happened to be fighting at that moment. The fact that Izanami was (in-universe) created solely for a very specialized purpose (countering the extremely rare Izanagi) yet turned out to also be the perfect counter to a completely different threat seals the deal.
At the climax of the 4th World War, Madara successfully captures all of the Tailed Beasts. This includes Naruto's Tailed Beast, and as a result, Naruto is left on the verge of death. A few minutes later, Sasuke attacks Madara, who proceeds to fatally stab Sasuke with nonchalance. With the two main characters on the verge of death, and Madara becoming a Jinchuuriki, he is very close to achieving his goal with nothing in his way, and all seems lost. Enter one Hagoromo Ōtsutsuki, the Sage of the Six Paths, a character who has only been spoken of in legend as well as from narrative from millenia-old beings, before popping up out of space-time to meet with Naruto & Sasuke. He proceeds to grant massive power-ups to Naruto (Juubi Jinchuuriki level abilities & a powerful seal) and Sasuke (Rinnegan & a powerful seal). Whilst the two are revived by other parties, Hagoromo appeared out of nowhere and gave them the means to defeat Madara & Kaguya Ōtsutsuki. A Hagoromo ex Machina.
Obito died, but turns out his eyes have the power to teleport the user from the afterlife back to the land of living as a chakra ghost, and then he passes both his Sharingan to Kakashi using chakra transfer. Mind you the Sharingan is a bloodline limit and his physical eyes were both destroyed when Kaguya desintegrated his body. And then Kakashi fully manifests a Susanoo in its stabilised perfect form in the first try. This isn't even getting started on the fact that Kakashi is able to use the Uchiha bloodline technique Susanoo, despite the fact that he, you know, isn't an Uchiha.
One Piece: In the Loguetown arc, Luffy is caught off guard and captured by the Buggy Pirates, who want revenge for an earlier defeat. As Buggy prepares to execute Luffy in front of a huge crowd while his friends try to no avail to save him, the entire platform is struck by lightning (which does not damage Luffy, a Rubber Man) just before Buggy can decapitate him, which frees him. This is lampshaded by Sanji, who then asks Zoro if he believes in a higher power. Though there is a possible subversion in that Luffy's Disappeared Dad, Dragon (who was present at the time) is hinted to have some kind of control over the weather, and thus may have purposely created the lightning strike in order to save his son, this has not been proven, and since fate plays a very important role in Luffy's journey, the trope very well could have been played straight after all.
Any situation involving a showdown between Team Rocket and "the twerps" where either Team Rocket seems to have the upper hand or the two sides have been forced into a dangerous stalemate. Cue a single, recurring Pokémon, typically either Marker-Jigglypuff or Misty's Togepi. The former will sing their soothing music and cause everyone to fall asleep (thus enraging it and causing it to doodle vengefully on everyone), or the latter will start using the Metronome attack, which causes a burst of random Deus Ex Machina energy to fill the room and set everything right. Metronome in the games is a completely random attack, selecting from a list of the majority of other moves in the game and naturally having a very high chance of doing something useless or detrimental. This never happens in the anime.
May's Skitty has the Assist technique, which randomly uses an attack known by another member of the party. Of course, it naturally has the Random Number God on its side. She got better about it, and later seemed to use it as a jump-off for improvisation than a lucky shot. One contest had her focusing on keeping Skitty alive while spamming Assist continually, producing effects varying from mildly useful to downright inhibitive, until she got the attack she wanted in the first place and oneshot the opponent.
There was one episode where Team Rocket grabs Pikachu and flies off in their balloon. How does Ash get him back? He jumps five stories straight up into the balloon basket, with no assistance from any nearby plot devices. It looked exactly as ridiculous as it sounds.
Pokémon: The First Movie features Ash running between a beam struggle between Mew and Mewtwo that turns him to stone. When a few shocks from Pikachu make it clear that Ash is, in fact, dead, all of the Pokémon cry... and their tears swirl over to Ash's body and bring him back to life. Nowhere else in the entire series is the fact that Ash was literally brought back to life brought up. Justified as in the prologue of the movie, it is explained that the tears of Pokémon contain life. This is also briefly mentioned in the movie itself. But only in the dub.
Pokémon 4Ever has a pretty bad one. After a long, heartwreching sequence of everyone sobbing over Celebi's death, several other Celebi come right the hell out of nowhere to bring the dead Celebi back to life, then they fly off never to be seen again. They were never mentioned before or even after this scene.
Pokémon Ranger and the Temple of the Sea has a similar occurrence where Ash suddenly gains what seem to be Dragon Ball powers to stop what would have otherwise been a villain victory. The original version had an unclear explanation and the dub added a slightly deeper level of justification.
There's a subversion in the Ash vs. Paul full battle by Lake Acuity. Even though Ash's Chimchar evolves into Monferno after beating Paul's Ursaring, it's unable to beat his Electabuzz. Though even if it had been able to, Ash would've lost eventually because Paul still would have had three Pokémon left.
Another example was Ash's battle against Tate and Liza, where Ash's Pikachu and Swellow, the last of which was at a disadvantage against their Lunatone and Solrock, inexplicably pulled out the infamous golden "thunder armor" gambit and knocked their opponents out.
Pikachu defeating Brock's Onix because he Thunderbolts it while the sprinkler system is running. Ironically, the video games would vindicate this years later with the introduction of the "Soak" move, which changes the target's typing to pure Water, with the predictable results. Of course, Pikachu can't learn Soak, but using the sprinklers to soak Onix in a more literal sense is a fair stand-in.
Pokémon: Hoopa and the Clash of Ages takes this to its logical extreme when Arceus itself, who made no prior appearance in the movie, shows up right out of nowhere to save the day and solve all the leftover problems.
In Pokémon Adventures, Ruby can't penetrate through the lightning that a machine made to be able to defeat the Big Bads. What does he do? The only logical thing, of course: call out Celebi, which doesn't make sense because Celebi is no more resistant to electricity than Swampert, but that's not all. Then Celebi proceeds to use its time powers to revive Norman, Steven, and Courtney. And Celebi's not even caught in a GS Ball, which the Mask of Ice needed a full blown out plan to get!
Justified and subverted in Puella Magi Madoka Magica. At first, it would seem completely coincidental how Homura seemed to arrive on the screen to save the day it seemed, as well as extremely unlikely. It turns out, however, that she is a Time Traveller and had repeated the same span of time over and over again, knowing what events were to happen and when the events would occur. With her power over time, she could appear when it is thought to be very unlikely.
A literal Deus Ex Machina is attributed to everyone's survival after the Final Battle. This despite several characters using a Dangerous Forbidden Technique to win their battles. The characters theorize that since they saved the world, the world decided to save them back.
Back in vol. 16, Musica and Reina are fighting against Orge, who has a Dark Bring that nullifies all physical attacks and wields a more powerful version of their silverclaiming technique, all while the superweapon Silver Ray is about to destroy the continent. The day is only saved by the hitherto-unmentioned silver claimer move known as Silver Bonds. While it does makes some sense that this move wouldn't have come up since there hadn't been another silver claimer in the group before, it still proves almost too convenient in that it's just what they need to kill Orge, stop the Silver Ray and resolve all the Ship Tease that had been building up between Musica and Reina. Well, it wasn't perfect since Reina still ended up dead, but it came really close.
Rozen Maiden was Cut Short by LaPlace announcing that the Alice Game of that era had come to an end, leaving all the action that currently was building up gone by a bloody rabbit deciding that the game will not continue within the very timeframe of the story, inevitably leading some fans to believe that they will never find out who wins. However, with the reboot of the manga and the "tales" being released on a monthly basis, this theory is thrown out the window, since the same dolls now appear in an alternate timeline in which Jun chose not to wind up Shinku. Indeed, it is too revealed that it was more LaPlace speaking in riddles, as he usually does. Indeed, the events of the original timeline did, in fact, happen, and the two timelines are revealed to actually be connected.
The Rozen Maiden anime's second season, Traumend, also ends with a major Deus Ex Machina. All of the dolls are defeated in the Alice game, and Barasuishou becomes Alice. Just when everything looks lost, she suddenly starts to crumble apart. This is explained along the lines of "she can't handle the purity of Alice", or something like that, as she's not really a Rozen Maiden. The dolls killed by Barasuishou come back to life. Those killed by legitimate Rozen Maiden stay dead.
Gensomaden Saiyuki: When outnumbered in a deadly pinch, Goku's diadem will break and he transforms into the Seiten Taisai. After kicking everyone's ass, he turns on his own friends until Kanzeon Bosatsu shows up and places a new diadem on his head.
s-CRY-ed has an episode in which Ayase is battling Kazuma. While fighting, she has a heart monitor reading her brother's life signs. However, when her bro kicks the bucket, she throws the fight and somehow loses the will to live and just dies.
Played absolutely straight in Slayers NEXT. Nearly the entire plot revolves around Lina's refusal to cast the Giga Slave after her discovery that miscasting it may end the world. Hellmaster Phibrizo eventually blackmails Lina into casting it and ensures that the casting fails, only for the power called upon by the spell, the supreme creator goddess of the Slayers universe, the Lord of Nightmares, to take Lina's body as an avatar instead and promptly annihilate the previously invincible (to the heroes) demon lord with a casual gesture. She also plays Reset Button by bringing everyone back to life that Phibrizzo had killed (Lina's breaking point about casting the spell was his threat to obliterate their souls as well).
Sonic X has one of these in the finale of its final season, where the stone Cosmo has been wearing since the beginning of the series is revealed to be a magical amulet that can automatically accelerate her growth so that she reaches the stage of becoming a tree (as is apparently the fate of all her species) early, attaches herself to the bad guy and weaken him so that the Good Guys can shoot and destroy. We had heard nothing about this earlier in the series.
Gurren Lagann did this over and over... sort of. Essentially a "logical" Deus Ex Machina was set up for the show's entirety with Spiral Energy, literally giving characters the ability to do the impossible (the chance of Kittan's giga-drill that freed the crew from the spiral-draining sea thing succeeding was given as 0% but through a great speech and shouting he succeeded) through their sheer willpower and greatness. On paper it sounds like an extreme Deus Ex Machina, but when watching/reading it it's exciting and used enough to not feel like the giant cop out it may first appear. Gainax being Gainax, they then hang a lampshade in the last act of the anime that is summated "using Spiral Energy too much will destroy the universe" (read: "using this too often can ruin a series").
Occurs in all three installments of the Transformers Unicron Trilogy; at some point the Autobots are defeated and critically damaged, but then they are repaired and upgraded (and in the third installment given new vehicle modes), by the Minicons in Armada, then by Primus in Energon and Cybertron.
In an earlier series, this is what saved Star Saber from Deathsaurus in Transformers Victory. Deathsaurus delivers a vicious, merciless beatdown, driving Star Saber to the point of deactivation. He's about to deliver the final blow when his living metal-destroying cannon... runs out of batteries.
Another example comes from Transformers Zone: Metrotitan is devastating Earth with a freeze gun, and Dai Atlas and Sonic Bomber are for some reason powerless to stop him. All of a sudden, Road Fire appear, with a heat ray that's just the thing to revert Metrotitan's effects, and then proceeds to single-handedly kick Metrotitan's retrocharger.
Star Blazers: The Comet Empire War; The near-Godlike Treleina of Telezart turns up at the very last moment to obliterate Prince Zordar's warship and save Earth. Subverted as Captain Wildstar had already begun the process of sacrificing the Argo in a ramming attack to achieve the same end.
At the end of Wolf's Rain, after Darcia defeats and kills all the major cast members and prepares to enter paradise, he is suddenly vaporized (except for his eye) for no apparent reason, other than he's evil. This comes off as a bit of an Ass Pull for some.
The heroes in Yu-Gi-Oh! seem to win solely on pulling the one card out of a forty card plus deck that can save them from doom. Many times, these cards are not alluded to prior to their save the world moment and turn the tide of the battle completely 180 degrees. After all, how many times have you heard the line "It all comes down to this one card" only to have them draw a complete waste of a card?
In the duel between Yugi and Mai in the Duelist Kingdom arc, Yugi wins by playing "Black Luster Ritual", which allows him to summon a more powerful monster than anything Mai has. Yet for some reason, only Yami is even aware that Yugi has it in his deck; Yugi has never heard of the card before.
In Tea's duel against Krump in the Virtual World arc, her Deck Master, Dark Magician Girl has three different abilities, each more inexplicable than the last. First it has the ability to telepathically communicate with Tea, allowing it to coach her through the duel. Then it has the ability to let her draw four new cards, and finally it lets her summon Dark Magician from Yugi's deck, despite that he wasn't even involved in the duel and just happened to be standing nearby...
Taken to its logical extreme at the end of the battle against Noah. Yugi's hand is empty, but on his final turn, he manages to draw a card that lets him draw six more cards. And, as it turns out, these were exactly what he needed to pull off a very specific combo attack to deplete Noah's 10,000+ life points. If not for The Power of Friendship scene just before, that draw would have been ridiculous even by Yu-Gi-Oh standards.
Taken even further in the duel against Leon in the filler tournament arc. Thanks to the Big Bad hacking the game system, Leon's Golden Castle of Stromberg forced Yugi to throw out half his deck at the beginning of every turn. This continued until Yugi only had one card left in his deck. This card allowed him to destroy all of Leon's monsters and all of his life points at the same time.
Kaiba's winning move against Zigfried in the same arc qualifies too. By using Zig's own Magical Alms card against him with a great deal of luck, he's able to draw five new cards, increase his Life Points enough to spend the amount needed to banish five of his Dragons and then summon all five of them, then launch an attack that blows Zig's monster to Kingdom Come and Zig's Life Points to zero. (And it was likely the most spectacular finish of Kaiba's career.)
In the last duel of the Battle City Final Yugi plays Ragnarok, a previously unseen card, which allows his entire cast of monsters to pulverize the Winged Dragon of Ra, and leaving Dark Magician and Dark Magician Girl on the field. The card was never played or mentioned again. (But it was kick-ass awesome.)
All of the Millennium Items seem to have a bunch of random powers that either activate by themselves, or the characters remember just in time. Of course those powers are never used again. For example, in one episode, Yami uses the power of the Millennium Puzzle to force the spirit of the Millennium Ring into the Duel Monster card he trapped Bakura in, and restored Bakura to his body.
In Seasons 2 and 3, Marik's Millennium Rod likes showing Kaiba visions, since Kaiba owned the Rod in a past life. When Marik orders the Rod to show him those same visions, it doesn't obey him.
Some episodes attempt to justify this by having characters note they need the right card to turn the duel around, but they don't get it for several turns and they have to stall. And there are only 40-45 cards in the decks, if you stall long enough you'll draw what you need sooner or later.
If anything, all of this can be chalked to pre-emptive Diabolus ex Machina, that is, the opponents drawing into what they need first to push the protagonists into a bind, for the sake of Rising Conflict.
Yu-Gi-Oh!: Capsule Monsters has a literal example. When Yami is injured in the fight against the Five-Headed Dragon, the girl chosen as a human sacrifice prays for the Blue-Eyes to aid him, joined by the other villagers. It awakens and aids Yugi.
The card "Miracle Tuner - Savior Dragon" ("Majestic Dragon" in the dub) from 5Ds has earned the nickname "Deus Ex Machina Dragon" within the fanbase, as it's a card that appears in a character's deck when the Crimson Dragon (the resident God for this series) wants it to. Not only that, but it allows whichever character that uses it to summon another monster that isn't actually in their Deck (well, Extra Deck technically, but still).
In Yu-Gi-Oh! ARC-V, main protagonist Yuya creates the new Pendulum Summoning method right out of the blue, allowing him to win a Duel. However, as this happened in the first episode, the series heavily deals in what happens afterwards. Yuya doesn't fully understand how Pendulum Summoning works, and he loses several off-screen Duels trying to figure it out. In addition, other people accuse Yuya of outright cheating, since his are the only Pendulum cards in the whole world, though the Leo Corporation eventually remedies this by manufacturing more.
Yusuke winning Genkai's tournament could apply. Ignoring the fact he was lucky enough to have Kibano tell him about his helmet, the editeddub qualifies because it removed the cigarette that led to his victory. Kazemaru lost because the throwing stars locked on to his energy at the same time Yusuke slipped into the mud; Genkai acknowledged that victory was a fluke. Rando attempts to shrink Yusuke the same way he did to Kuwabara, but it backfires. Genkai explains that a chant will do so if it can't be heard by the victim and it turns out at that moment Yusuke had algae in his ear.
Another one from the Dark Tournament: Kuwabara is in a fight that he knows he has no chance of winning (for reference, he was screaming in pain on his way into the ring) and is planning to kill them both with a suicide attack to win, (his team has four wins and the other only has two, so a double win will bump them up to the necessary five). Suddenly, Yukina arrives which somehow restores Kuwabara's energy and he knocks his opponent across the stadium with one shot.
From Chapter Black, Yusuke's fight with the Doctor contains three of these in a row. The first, and most random, happens when the Doctor takes a female nurse hostage who turns out to be a disguised (and sickly) Yanigisawa who manages to save himself. The second happens when he tries to fool Yusuke with a false antidote to his plague which gets ruined by the sudden appearance of Murota (also sickly). And the final one happens when Yusuke seemingly kills the Doctor (as the only way to stop his plague) only to have Genkai revive him.
There's also Hiei deciding to helpprecisely when Sniper blows up the truck. This one had been foreshadowed by Kurama, who had declared that Hiei was just posturing when he said he wouldn't help, and was proved right when Hiei got a flimsy justification and entered the frame.
Also Yusuke being resurrected after being killed by Sensui due to being a descendent of a powerful demon king. Afterwards Sensui was still stronger and more experienced with his level of power and Raizen takes over Yusuke's body to completely dominate Sensui who at that point was dominating the fights before.
Hunter × Hunter is a repeat offender of Deus ex machina, but one of the most striking examples is Alluka. She is a literal machine (machina?) of this trope. She has a special power that can supposedly do anything (the limits of this ability are unknown by anyone In-Universe, but Illumi speculated that there is probably 'no limit'). "It" never uses the ability itself, and only uses it when someone asks for a wish. There are strict rules regarding how to use the ability, and there are drawbacks in the form of a backlash, which can be trivial or severe, depending on the magnitude of the wish. Alluka was first introduced (with no hint of prior existence aside from confirmation that Killua had additional siblings that had yet to be introduced) after Gon sacrificed his aura to defeat Neferpitou and was left in a state of near-death with little chance of being revived through 'normal' means. Obviously the only point of bringing this character into the manga was to heal Gon and pretend that nothing ever happened. This is a wish that was expected to have an extremely major backlash that could potentially end up killing the entire Zoldik family, but, of course, it turns out that Killua can break the established rules for no reason and "command" Alluka to give any wish without any backlash.
In Planzet, the day is saved when the protagonists stumble onto a Super Robot that was hidden until it was absolutely necessary. Its origins are never explained.
In Fairy Tail, the guild is completely worn out after having fought all of Phantom Lord's best members and mooks, but their almighty leader is still in top shape. It's a good thing Makarov came back and destroyed them all with a single spell. Granted, Makarov coming back from his Game-Breaking Injury was foreshadowed throughout the arc with several scenes showing the guild's healer help him recover, but the singular spell? That didn't receive a thing.
The X-Balls, which provided a way for the Fairy Tail gang to regain their magic in Edolas. There's no hint for how or why Mystogan (who gave them the X-Balls) would have them aside from him being from Edolas, but even then there's no explanation for how he created them.
Mavis' Fairy Sphere saves Sirius Island from the Diabolus ex Machina of Acnologia's attack. However, Mavis won't be able to use it again, and the guild was still split apart for seven years.
In the Tartarus Arc Mard Geer uses the curse Alegria that froze everybody inside the Tartarus' base. Everybody except Lucy. Mard Geer even said that the chances to not get caught were one in 1,000,000,000. And Lucy conveniently was the only Fairy Tail wizard that could summon the Celestial Spirit King that knew exactly how to dispel Alegria which released all of Fairy Tail and allowed them to defeat Tartarus and stop Face.
In the same arc, when all the 3,000 Faces were about to activate and destroy all magic of the continent, the dragons, the same that raised Natsu, Wendy, Gajeel, Sting and Rogue, and disappeared several years ago, all appear from where they were hiding inside their Slayers and destroyed all the Faces.
There are quite a few glaring ones in the Alvarez arc, so much so that the term has been affectionately renamed "Deus Ex Mashima":
Gajeel survives being dragged to his certain death thanks to the timely activation of Irene's Universe One.
A rejuvenated Dimaria Yesta, with no-one left on Fairy Tail's side to oppose her time stopping magic (due to Chelia losing the ability to use magic), is off-screened by the awakening of an E.N.D.-possessed Natsu after she attacks Lucy, and who is apparently so strong that he's immune to her power, something that Dimaria herself can only mutter in shock at.
Both Irene and August having last minute Heel-Face Turnsfor the sake of their loved ones and committing suicide to nullify almost 100% guaranteed victories (Irene about to kill Erza; August about to kill everyone not named Zeref or Acnologia).
In Doraemon: Nobita's Little Space Battle, the characters have been shrunk and the gadget they used to do so had been stolen, so they must take it back as it is the only way to reverse the shrinking effect - or wait for half a week, because apparently the effects of the shrink ray isn't permanent. Plenty of other times though it's been implied that it is everlasting. In fact, this is the only time that the effects of the shrink ray wear off in the show.
Fullmetal Alchemist. The result of the fight between Scar and King Bradley is decided by an almost literal one. Bradley has Scar dead to rights, and takes a moment to insult Scar's beliefs, telling him he's ridiculous for believing in God. At that moment in the sky, the solar eclipse ends and the sun's rays start coming out from behind the moon, glinting off of Bradley's sword and blinding him long enough for Scar to land a fatal blow. As he lays dying, Bradley can't help but note the irony of what he said.
Vampire Knight: At the end, the solution to coexistence is a sudden discovery of an old theoretical cure that can transform vampires into humans.