The Third Oath, from The Zombie Knight is by far the darkest section of the story (so far). In one day, most of Hector's friends are murdered and have their souls eaten, and the few that survive blame him.
Micheal Grant's Gone series has this at the end of Fear, where the ending is that the FAYZ wall is transparent.
Plague would be a straighter example what with Diana, Albert and Quinn changing sides, Little Pete "dying", Astrid leaving Sam and Caine taking over Perdido Beach.
The revelation of further members of the Glaw family, working for the Emperor's Children to boot
Sister Bismillah revealing that she is actually MedeaBentacore, observing Alizebeth undercover for her boss.
The revelation that Beta is likely a clone of the original Alizebeth Bequin.
The best one yet:
Deathrow:I am Alpharius.
The Wheel of Time manages to pull this off in several installments, most notably the endings of books:
2: Rand revealing himself as the Dragon Reborn by fighting in the sky with Ba'alzamon.
3: The claiming of Callandor and Rand actually declaring himself the Dragon Reborn.
6: The battle at Dumai's Wells and the aftermath where the Aes Sedai swear fealty to Rand.
And especially 9: the cleansing of the taint from saidin.
Cranked Up to Eleven in 12 with The Prophet getting executed by Faile in the prologue; Verin's true allegiance; Egwene fending off a huge Seanchan attack on the White Tower, executing nearly the entire Black Ajah in a single day and FINALLY becoming Amyrlin of a united Aes Sedai; Rand killing both Semirhage and Graendal, starting to use the True Power and destroying the Choedan Kal. Robert Jordan was quite good at these.
Note that the events of book 12 were technically written (mostly) by Brandon Sanderson, though planned by the original author. Also, WHAM moments like these have become increasingly common since book 10 or so, as part of an earnest effort to prune the Kudzu Plot that's been building throughout the series.
And the Whams continue in book 13: Mat killing the gholam; Rand's incredible destruction of the hundreds of thousands of Shadowspawn attacking Maradon; Perrin stopping balefire with his wolfdream skills, and forging his new hammer; Egwene breaking Mesaana's mind; the future of the Aiel; the 13 x 13 trick being used at the Black Tower; the rescue of Moiraine, particularly with Mat's ashandareibeing the key out of the realm of the Finn; and especially the epilogue which reveals in rapid succession a new horrific form of Darkfriend, a huge army of Shadowspawn attacking Caemlyn, and Lanfear once more toying with Rand's mind.
A Storm of Swords, the third book of A Song of Ice and Fire, ends with many devastating events, including deaths of many major characters, with the revelation that a supposedly minor and rather affable villain was actually behind everything, and the resurrection of a character who had been killed earlier in the same book. This was originally meant to set up for a five-year timeskip. When the author couldn't get it to work, the rewriting of the plot ironically caused a five-year delay for the next book.
The first book's ending arguably contained even more WHAM, what with the grand execution and all...
Northern Lights ends with Lyra's realization that she had traveled so far, and gone through everything, just to ultimately give her father Roger as a human sacrifice. Lord Asriel kills him to rip open the boundaries of their world, revealing that the carefully crafted fantasy world that the book has been entirely set in up to that point is actually one of many — and that our world is also one of them. Then he declares war on God.
The even bigger Wham in this event was when Asriel and Coulter, supposedly deadly enemies, run to each other and have a lovers' embrace, less than a minute after Roger's death. Their previous behavior throughout the entire book was suddenly cast in a very different light.
Sorcerer's/Philospher's Stone starts a series of wham endings right off the bat with the final chapter revealing that Snape was a red herring; he wasn't trying to kill Harry, he was trying to save his life. Instead, Professor Quirrell, the supposed cowardly sad sack, was in fact the person setting the chain of events off. Oh, and the chapter title, The Man with Two Faces? That's not metaphorical, Quirrell has Voldemort's face coming out of the back of his head!
The Chamber of Secrets has a couple: Hermione is petrified, Dumbledore is kicked out, Hagrid is sent to Azkaban, Ron's little sister Ginny has been taken into the chamber, and not only is Tom Riddle, who we thought was the hero of the last incident, behind everything, but he's also Lord Voldemort.
Prisoner of Azkaban reveals that Sirius was innocent while Peter Pettigrew, alias Wormtail/Scabbers, was guilty. Oh, and Professor Lupin is a werewolf.
Goblet of Fire has the scene in the graveyard, with Harry tied to a gravestone, Voldemort taking his blood, all sorts of other hideous stuff, him seeing his parents, priori incantatem, the list goes on, but what takes the cake was the first death: Cedric Diggory. It started the whole Anyone Can Die chain reaction. Almost all fans agree that this one chapter set up the Darker and Edgier vibe for the rest of the series.
Quite frankly, the fans agree on one single line that officially marked the transition from light and cheerful to dark and and edgy.
Order of the Phoenix reveals that it could have been Neville that the prophecy meant instead of Harry. Yes, that Neville.
Deathly Hallows has a good number of them, but special mention goes to the revelation of Snape's full backstory and motivation.
Dragon Age: Asunder is a massive one for the entire Dragon Age universe; in the space of one book, a Tranquil figures out how to cure Tranquility, and the Enchanters' Conclave, the Seekers of Truth, and the Templar Order all secede from the Chantry, all while Orlais is collapsing into civil war and rumors of an elven rebellion in the Dales are spreading.
Ashes of Victory in David Weber's Honor Harrington series upsets everybody's applecart at the end! First, a "chess fork" assassination attempt forces Honor to choose among the important figures she could possibly save, ultimately handing a government over to corrupt incompetents. Meanwhile, the Soviet/France-during-the-Terror Haven undergoes upheavals even more drastic, from an unexpected quarter.
As the Meta Plot of the series is a retelling of the great Anglo-French war IN SPACE!, this is based on the "Peace of Amiens" and the transition of power in France from the Committee of Public Safety to Napoleon I, and was planned out pretty much from the start. (With a few minor surprises here and there, anyway.)
Similarly, the scene in Mission of Honor where Oyster Bay happens, and of course the very final chapter of the book which re-aligns the political and military framework of the entire series over the course of a conversation.
While the other novels work well with plot twists, the last quarter of the fourth Temeraire novel, Empire Of Ivory, is probably the most staggering example. It sees the destruction of every English port in southern Africa by an army of dragon-riding tribesmen; a plan to effectively commit genocide upon the other dragons of Europe by sneaking an ill dragon into Napoleon's air corps, which would spread the plague that nearly wiped out England's dragons throughout the entire Eastern Hemisphere, but also would surely provoke a bloody invasion attempt by Napoleon; and Laurence and Temeraire committing treason to deliver the antidotal mushrooms to the French forces before it's too late. The end has Laurence and Temeraire returning to England, to what will surely be Laurence's court martial and hanging.
Dragonlance is nothing but a Wham series. In reciprocation. Over millennia and-one-hundred-or-so books: Sturm is Huma's carbon-copy, The draconians are hatched from the supposedly-protected eggs of the good metallic dragons, Raistlin literally is Fistandantilus, Fizban is Paladine, Berem is responsible for the entire Second Dragon War, Par-Salian's version of 'The Test' breaks Raistlin, Steel Brightblade is the son of Sturm and Kitiara, Tasselhoff is blessed by Paladine himself... and that's about 5% of the MAIN storyline, too. Also the Amber and Iron trilogy about Mina) contains a huge wham. In a tabletop-game world carefully balanced between good and evil, the idea that there's another goddess that nobody knew about, including her, is not just unexpected, it seems downright impossible.
The last few chapters of The Fall of Hyperion are all wham. First the Ouster invasion fleet turns out to have been flying at the Hagemony for centuries at sublight velocity to avoid detection, then we actually meet the Ousters and the "invasion fleet" turns out to be a fleet-full of cybrids sent by the Core, who turn out to be located inside the Portal Network, leaving the only solution as the destruction of said network, and as such human civilization. Somewhere in the middle of all this, Kassad goes toe-to-toe with the Shrike. And then the Time Tombs open, and we find out who Moneta really is.
Star Trek: Destiny, in which the Borg launch an invasion of the Alpha Quadrant, destroying several dozen worlds and annihilating forty percent of Starfleet, before every single drone is liberated all at once, wiping out the collective once and for all.
The Pillars of the Earth takes a hard left turn when William raids Kingsbridge, nearly burns it to the ground and kills dozens, including the book's main character.
Animorphs, Book 23, The Pretender: Tobias learns that Prince Elfangor, the Andalite which gives the five humans their ability to morph, was his father. Sort of. All the more gut-wrenching because the entire plot of the book was, up that point, about him possibly finding a home and discovering it was a just a ploy by Visser Three to see if he knew anything. Guess which character is The Woobie in the series?
The next book has an even bigger one: Cassie prevents Jake from killing Tom, allowing the latter to escape with the morphing cube.
#5, too. Sorry Marco, you're gonna need to kill your mama, at least twice.
The last two chapters of Mistborn: The Original Trilogy} book two. Everything that happened in the story up to this point was a Xanatos Gambit by the real, godlike Big Bad. The world is ending, everything you know is a lie, the prophecies are wrong and reality has been edited. Good luck. There are more than enough clues up to this point for the reader to figure out that things aren't quite as they seem, but nothing will prepare you for this.
Right smack dab in the middle of The Accidental Mage, when Gerald nearly gets his soul ripped out of him by Lional. I mean honestly, we knew Lionel was up to something, but this!?
In the Vorkosigan Saga, the beginning of Memory, when Miles gets kicked out of ImpSec for falsifying a report.
The end of The Fire Dragon, the 11th book in the Deverry series. Rhodry being transformed into a dragon is a complete surprise, given how difficult Shapeshifting has been shown to be.
The end of Dead Beat in The Dresden Files. So far the series had been about a Occult Detective. There were always acknowledgements of a Balance Between Good and Evil, and wizarding politics were often a problem for Harry, but for the first six and a half books of the series Harry was a detective who happened to investigate vampires in addition to mobsters and to carry a staff in addition to a revolver. Then, at the end of book seven, Harry is recruited into the Wardens because over half the organization had been slaughtered by a blitzkrieg in their ongoing war with vampires. Shortly after that, Harry deduces that his Monster Of The Weeks weren't just sorcerers feuding with each other but were fighting over enough power to become Physical Gods. At the end, he points out that his enemies had probably been allied to the vampires all along. Since then, the series has more been about wizarding world problems than his investigation business, even if that's how the story gets started sometimes.
Changes. There's a very good reason that this is the first book in the series to not have a two-word Punny Title: the entire book, in a very big way, is basically a wham episode. We find out that Harry has a daughter and that his mentor Ebenezar McCoy is his maternal grandfather. Harry's office, his car, and his apartment are all completely destroyed, along with almost all of his possessions. The White Council is on the verge of disintegrating; Ramirez and many of the younger Wardens have been imprisoned by the Council, and Luccio and a number of other older Wardens are missing. Harry accepts the position of Winter Knight, Susan dies at Harry's hand, doing so in a way that takes THE ENTIRE FREAKING RED COURT with her, he finally makes a date with Murphy, and the book ends with Harry being shot in the chest and falling into a lake, his exact fate unknown. Then the next book got announced: Ghost Story - Harry's DEAD. Oh, and Harry's duster gets destroyed. The whole book qualifies as a Cluster Wham Bomb.
The next book, Ghost Story, goes even further. Supernatural powers are running around snatching up whatever bits are left of the Red Court's former power base, leading to covert wars in the streets with the White Council locked up just trying to keep order. The Corpsetaker is back and is pissed. Bob's evil side is going completely Red Skull. Molly has gone almost completely off the deep end thanks to the trauma she took in the final battle in Changes and from erasing Harry's memories. And Harry discovers who had him killed: He did it to himself and had Molly erase his memories of setting it up, so she now has to live with the knowledge. And at the end of the book, he takes up the mantle of Winter Knight willingly, but not without telling Queen Mab where she can stick it.
Cold Days throws even more curve balls at the readers. Demonreach is a prison for dark gods created by Merlin. An entity called Nemesis is behind the Black Council, and can infect people's minds to twist them to its cause. Maeve has been so infected, and kills Lily before being killed as well, with Molly becoming the new Winter Lady.
"Killers of the Dawn" has Steve Leonard revealed to be a half-vapaneze, before he initiates a manhunt of Darren and his companions (while slaughtering his way out of a hospital), and it ends with Mr Crepsley having a Heroic Sacrifice where he kills the Lord of the Vampaneze...only for his sacrifice to be rendered pointless when Steve reveals that he is the Vampaneze Lord.
Also, we find out that Darren's faithful Little Person companion, Harkat Mulds, was, in his previous life Kurda Smahlt - a vampire traitor.
"The Lord of Shadows" has the revelation that no matter who wins the war, either Darren or Steve is destined to become a raging and powerful tyrant, who will destroy their own clan, conquer the world, and turn it into the Bad Future at the same time as Steve invades his and Darren's home town, begins massacring people (including one of their childhood friends), murders the infant son of one of Darren's friends, and reveals that his own son is Darren's nephew.
And, in Sons of Destiny, Mr Tiny reveals that Darren and Steve are not only brothers, that they are also his own two sons.
The ending of Tom Clancy's Debt of Honor: After being confirmed as Vice-President, following his predecessor being forced to resign by a sex scandal, Jack Ryan narrowly escapes a terrorist attack that kills that kills almost every major politician in the U.S. Capitol building (including the President, most of Congress, most of the Cabinet, the Joint Chiefs of Staff and every Supreme Court Justice). Ryan is then immediately sworn in as President moments later by a federal judge not present at the Capitol Building.
Codex Alera has Princeps' Fury: Canea is overrun by the Vord, and so is half of Alera. Gaius Sextus obliterates Alera Imperia when the Vord overrun it, and dies in the process.
Warrior Cats, being a long running series, has had many shocking developments among its plentiful installments:
Into The Wild:
Chapter 4: Ravenpaw arrives in the ThunderClan camp and announces that Redtail and Oakheart are both dead.
Chapter 8: It's revealed that Yellowfang, the cat who attacked Firepaw is the ShadowClan medicine cat. Then, Bluestar learns that Firepaw broke the warrior code and unleashes her fury on him.
Chapter 12: Brokenstar is introduced as the Big Bad, and he reveals that not only has he driven out WindClan, he'll be coming for anyone who doesn't bow down to him. Then, he whips the ThunderClan warriors into a rage against Yellowfang, and they decide to attack her.
Chapter 17: ShadowClan attacks ThunderClan and kills Lionheart. Then Tigerclaw is named deputy, while Ravenpaw reveals that he may not be on ThunderClan's side.
Chapter 20: Ravenpaw reveals that Tigerclaw killed Redtail because of his ambition, and he'll be going after Bluestar next. Then, Spottedleaf is found dead, Frostfur's kits are stolen, and Yellowfang mysteriously vanishes.
Chapter 22: Firepaw and Graypaw confront Yellowfang, who reveals the true plans Brokenstar has for the forest.
Fire and Ice
Chapter 1: Fireheart finally reveals Tigerclaw's treachery to Bluestar, but she doesn't believe him.
Chapter 7: When taking a shortcut back to ThunderClan territory, Fireheart and Graystripe accidentally cause a massive border battle and a RiverClan warrior is killed.
Chapter 9: Fireheart is revealed to have a sister who lives near the forest.
Chapter 14: Graystripe is seeing a RiverClan warrior! And she's the Clan leader's daughter!
Chapter 17: Cinderpaw is hit by a car, and Yellowfang says that she'll never be a warrior.
Chapter 26: Brokenstar attacks the camp, and Yellowfang reveals that he is her son.
Chapter 30: ShadowClan finally allies with RiverClan and a huge battle between all four Clans breaks out on WindClan territory.
Forest of Secrets
Chapter 6: Graypool reveals that Mistyfoot and Stonefur were actually from ThunderClan, and Fireheart vows to learn the truth.
Chapter 11: A massive flood begins, and a RiverClan kit is swept up in it.
Chapter 19: Nightstar reveals that ThunderClan is sheltering Brokenstar, causing ShadowClan to team up with WindClan and begin an invasion of ThunderClan.
Chapter 21: Silverstream dies while having Graystripe's kits, and Tigerclaw finds out about Graystripe's forbidden romance.
Chapter 23: Bluestar reveals that Oakheart was once her mate, and that Mistyfoot and Stonefur were her kits.
Chapter 30: Rather than cause a Clan War, Graystripe decides to leave ThunderClan and join RiverClan.
Chapter 5: Mudclaw ambushes Fireheart and Bluestar on the way to the Moonstones, declaring that ThunderClan no longer has the right to visit StarClan.
Chapter 12: Cloudpaw is captured by Twolegs and taken away.
Chapter 16: Tigerclaw reveals that he now leads Brokenstar's rogues before threatening Fireheart.
Chapter 27: Fireheart finds Yellowfang in the ashes of the ThunderClan camp, only to be too late to prevent her death.
Chapter 30: ShadowClan has a new leader. It's Tigerclaw!
A Dangerous Path:
Chapter 7: Graypool accidentally reveals Bluestar's secret to Tigerstar, then falls to her death.
Chapter 16: To protect Bluestar from Mistyfoot and Stonefur, Fireheart reveals that she is their mother.
Chapter 19: Swiftpaw is brutally killed when he tries to fight the dogs, while half of Brightpaw's face is ripped off.
Chapter 24: Tigerstar murders Brindleface to lead the dogs to ThunderClan.
Chapter 27: Tigerstar attacks Fireheart at a crucial moment, forcing Bluestar to sacrifice herself and save him.
The Darkest Hour
Chapter 4: Fireheart has his leader ceremony, only for it to be hijacked by an omen of Tigerstar's power.
Chapter 8: Darkstripe feeds Sorrelkit deathberries to prevent her from revealing Tigerstar's plans.
Chapter 12: Tigerstar reveals his plans at a Gathering, uniting with RiverClan to force ThunderClan into checkmate.
Chapter 15: The Bonehill actually shows up, and Blackfoot murders Stonefur on Tigerstar's command.
Chapter 19: Tigerstar leads an attack that devastates WindClan so that Firestar will know that he's next.
Chapter 22: Scourge hijacks the book by killing Tigerstar and declaring that he now rules the forest.
Chapter 24: Barley reveals that he was once a member of BloodClan, before revealing the horrors of Scourge's reign.
Chapter 28: Bone kills Whitestorm during the battle. Then, Firestar tries to take on Scourge, only to get himself killed.
Chapter 1: Since the series has had a pretty big Time Skip, we end up with a big one. Brambleclaw gets a vision from Bluestar, and we're introduced to Firestar's daughter Squirrelpaw.
Chapter 3: The point of view shifts to Firestar's other daughter Leafpaw, and we learn that RiverClan has taken in two former rogues, Hawkfrost and Mothwing.
Chapter 8: Leafpaw and Cinderpelt find a prophecy about how Brambleclaw and Squirrelpaw will destroy the forest.
Chapter 13: Brambleclaw, Squirrelpaw, Feathertail, Stormfur, Crowpaw, and Tawnypelt leave Clan territory and head into the unknown, a first in series history.
Chapter 20: An old cat called Purdy leads the band astray, ad they get ambushed by rats.
Chapter 24: Midnight is actually the name of a badger. And she reveals that the forest is doomed.
Epilogue: The destruction of the forest begins.
Prologue: The Clan cats are not alone. A new group of cats called the Tribe of Rushing Water is revealed to be living in the mountains.
Chapter 5: The band gets hit by a waterfall and their fate is left unknown.
Chapter 7: The band meets the Tribe of Rushing Water for the first time.
Chapter 14: The story moves to the point of view of Feathertail when the Tribe abducts Stormfur. Then, Sharptooth appears and begins his attack.
Chapter 19: The rebellion against the Tribe begins. As well, the Clan cats decide that they have to defeat Sharptooth once and for all.
Chapter 21: Mothwing reveals that Tigerstar is her father, and the father of Hawkfrost.
Chapter 23: Feathertail realizes that she is the cat destined to defeat Sharptooth, giving her life to save Stormfur.
Chapter 24: Leafpaw is abducted by Twolegs as the end of the forest draws near.
Prologue: Things get even worse for the forest when Fourtrees falls, after standing for many years as a symbol of the Clans.
Chapter 5: Leafpaw meets Sasha while in Twoleg captivity.
Chapter 7: The Clans attempt a rescue mission for the cats in Twoleg captivity, but Graystripe is captured, and will likely never be seen again.
Chapter 14: Firestar loses a life helping ShadowClan, while Crowpaw goes suicidal.
Chapter 16: Mudfur dies, leaving Mothwing as RiverClan's sole medicine cat.
Chapter 19: The Clans receive a sign telling them their new home lies across the mountains.
Chapter 25: The Clans find their new home and Leafpaw stares down as the stars appear overhead.
Chapter 3: The new homes of the Clans are finally revealed.
Chapter 6: Tallstar dies and names Onewhisker deputy while on his deathbed.
Chapter 14: Brambleclaw meets Hawkfrost in a dream. And who summoned them? Tigerstar, and he's out for revenge.
Chapter 16: Mothwing reveals that she doesn't believe in StarClan. And she's a medicine cat.
Chapter 19: Leafpool has a horrifying vision of the lake turning red with blood.
Chapter 22: Leafpool nearly gets killed by two warriors, but Crowfeather rescues her and they admit their love for each other.
Wizards At War (from the Young Wizards series) was basically one long Wham Episode, tying up several ongoing plot threads and starting nearly double as many, as well as building up Dairine and Roshaun's relationship only to have Roshaun disappear mysteriously; causing Ponch to ascend to a higher plane of existence; creating a whole new version of the Lone Power called the Hesper, a version of the LP that never fell; and then completely *not* resolving the UST between Nita and Kit.
The eighth book, Last Stand of Dead Men is this. That's right, the entire book. but Chapter 51 in particular. that one hurts every time.
"Invisible Monsters" has a few of these, such as the true identity of Brandy Alexander being the main character's brother and who shot the main character - she shot herself.
For Gaunt's Ghosts, the biggest one is probably at the end of book four, The Guns of Tanith. Dan Abnett says that to this day he still gets mail about it. It is, in his words, where "you learn to say goodbye", representing the series passing into the realm of Anyone Can Die, and is in fact the source of the page quote for that trope.
Special props go to Kathy Tyers' Daystar. The fact that it is about Jesus in an alternate 'verse means it is chock full of Foregone Conclusions, and yet it still pulls off a major wham ending: Everyone has had a chance to hear the Word and to choose their side, so the cosmos is renewed then and there.
The new Big Bad is revealed to be Gaea, goddess of the Earth itself.
The Mark Of Athena:
Chapter 4. The Argo II has arrived at Camp Jupiter, and so far, things are going well. Annabeth and Percy are reunited, Octavian is keeping his mouth shut, and Annabeth and Rayna are getting along. Then the Argo II opens fire on Camp Jupiter.
The ending. The destruction of Rome has been averted, Nico is rescued, the giants holding him are dead, and the Athena Parthenos, the key to ending the rivalry between the Greek and Roman demigods, is secure aboard the Argo II. Then the floor crumbles, and Annabeth and Percy fall into Tartarus.
Cry, the Beloved Country, at the end of the second book. Absalom Kumalo is sentenced to death and Gertrude Kumalo is nowhere to be found. The revelation of the murder Absalom committed was a WHAM in itself.
The Agent Pendergast series has some major whams during the first and second books of the Helen Trilogy.
Fever Dream: Through the first half of the novel, Pendergast and his friend Lt. D'Agosta have been investigating the events that lead to the murder of Pendergast's wife, Helen. Pendergast informs his brother-in-law Judson Esterhazy, and Judson goes on what appears Roaring Rampage of Revenge killing anyone who could have contributed to her death. Then at one point Judson attempts to shoot and kill Pendergast, revealing his agenda is far darker than initially believed. D'Agosta winds up getting shot through the heart and nearly killed.
Cold Vengeance: The very last chapter. Pendergast is reunited with the still-alive Helen. Members of the Neo-Nazi society the Covenant track them down. Judson is killed in the crossfire, Helen is kidnapped by them, and Pendergast and his butler Proctor are both shot.
Into the Gauntlet: The main plot is resolved with the Cahills all working together to stop Isabel, then all giving their clues to Dan and Amy. But then we get a Sequel Hook: there's another important player, an evil organization called the Vespers.
The second series, Cahills vs. Vespers, gets several:
A King's Ransom: William McIntyre dies, starting the Anyone Can Die atmosphere. The Guardians are revealed, and Atticus is one. Then Atticus is kidnapped, and Dan gets a text from AJT.
Shatterproof: Erasmus follows Amato to the Vesper base, but she manages to kill him. Then Jonah and Hamilton show up, and Jonah shoots Amato. Furthermore, another big reveal happens in the online game, or the beginning of Trust No One for those who don't play it: Vesper Three is Sinead Starling.
Trust No One: After the aformentioned reveal, Isabel comes back. Then V1 says they're done with giving him stuff, after one more: the Cahill Ring. Then we find out what the Vespers are using all of this stuff for: They're building a Doomsday Device. Finally, in order to combat them, Dan drinks the Serum.
Around Chapter 17 of The Maze Runner, when Thomas jumps into the Maze with Alby and Minho. Alby has been stung by a Griever, and the doors to the Glade shut behind them, trapping the three boys for the night. The previous chapters weren't exactly pretty, but things get BAD at this point.