All prequel-style fan works struggle with this. For example, in Maurauder-era Harry Potter fics, everyone already knows that Lily and James will end up together and so will Frank and Alice, Snape will join the Death Eaters, Peter will betray his friends, Sirius will end up in prison and a lot of people will die...
Due to the author having written sequels for Alternative Class Despair before officially finishing it, the survivors are already known to be Chiaki, Nagito, Kazuichi, Mahiru, Ibuki, Nekomaru and Peko.
Brought up in the Supernatural/Sherlock fic "The Case of Identity Switch" after Dean Winchester and Sherlock Holmes swap bodies. When Crowley is summoned by Sherlock and Sam, he expresses knowledge of Moriarty, and when Sam asks if Crowley has a deal with Moriarty, Crowley affirms that he doesn't, but considering Moriarty's lifestyle it's not exactly likely that Moriarty will go anywhere else when he dies.
The Child of Love: The creator wrote an epilogue featuring a seven-years-old Teri and a one-shot set in Teris teen years, so that whoever reads the unfinished sequel already knows NERV wins the Angel War, Third Impact does not happen, and Shinji, Asuka, Teri, her brother, Rei, Misato and Kaji survive.
Chrysalis Visits The Hague: In the aptly-named chapter, Estermann Office Observation Transcript Excerpt from Tuesday, November 22, 2015, lawyer Alexander Estermann, judge Colm Mullan and Lyra Heartstrings swear each other to secrecy over the revelation of Lyra's true identity, as well Colm's and Estermann's secret meetings. However, considering the format of the chapter itself (a surveillance transcript penned by some mysterious third party that had been listening in on the conversation), this secrecy evidently does not last very long.
In most of the Pokémon fics, it becomes clear how things will play out depending on what the fic is adapting from primarily. For example, Truth and Ideals opened up with the Late-Arrival Spoiler from the games; Ash will catch Zekrom, and N will catch Reshiram, and both of them will have a conflict occur upon Team Plasma interrupting the Pokémon League. Everything that happens up to that point, aside from Ash winning the league in the end, was otherwise considered fair game in terms of what the author would change.
In the Digimon fics, everyone who canonically achieved final form in the series it's basing itself on will be able to either immediately or gradually become said final form in the fic, sometimes even going further and allowing partner Digimon to access their Mega Level forms whereas previously they would be left out of said privilege.
Wes' inevitable disruption of Cipher and the downfall of their Orre Branch is the inevitable; how everyone gets to that point is where things diverge from canon immensely.
The synopsis for A Cold Calculus tells us that Euphemia emerges from the story as Empress of Britannia. Also, the opening snippets (framed as a history book) gives the outcome of few story elements such as Viletta's becoming a Knight of the Round and Nina's research eventually leading to nuclear weapons development.
The Council Era is a Mass Effect fanfic centered on the Rachni Wars (in the first half, the 83 CE arc) and the Krogan Rebellion for both that and the 783 CE arc. In the first half, three species that don't exist in the video games are introduced. All three are, naturally, extinct by the end of the story. Other examples include: the krogan will be used to reduce the threat of the Rachni by the end of the first half (as stated in canon); the first half covers the build-up to the Krogan Rebellion, said rebellion will end with the genophage (a fertility plague that is killing off the Krogan in the games) being released (again, as stated in canon). These are bound to happen when you're writing a fic set in the past and intend to stick to canon. It doesn't lessen the drama of the storyline, though.
A Crown of Stars: The author informed upfront that this story was a Fix Fic; and in the first chapter Shinji and Asuka meet their future selves, so that the reader knows that whatever else happens in the history, Shinji and Asuka will get over their traumas at least partially, get together, get married and Shinji will get Asuka pregnant. The interesting part is HOW they get to that point despite being so messed-up when the fic begins.
This comes into play when Asuka is arguing with her inner side in chapter 59. Her turmoil mocks her that Shinji could be dead the next day. She starts arguing...and then she realizes she knows they will not die tomorrow. She knows where they will be six months from now. That knowledge helps her to defeat her doubts and fears.
Death Note Equestria is a retelling of Death Note translated to a different setting, so although there are some changes, you know going in certain things have to happen. For example, there's a good chance (depending on which version of Death Note is being discussed) that L won't make it out alive. She doesn't.
Escape from the Moon: In the sequel The Mare From the Moon, Twilight and the other characters have met the windigo Snöflinga, who tells them the true story of the events that led up to Equestria's founding. The story itself is told offscreen, but its events are depicted in the side-story A Winter's Tale, meaning it's a given that the story will end in Snöflinga being separated from his friends Pansy, Cookie and Clover, and buried in ice for over a thousand years while the trio successfully ignite the Fires of Friendship and become the founders of Equestria.
In Everywhere at the End of Funk, Boyfriend suffers from early onset dementia. Due to the nature of the disease, Boyfriend will eventually succumb to his condition, one way or another.
Due to this story's non-linear narrative, this happens a lot.
The first chapter happens in 2020. Shinji and Asuka are alive and together. In a later chapter, set in 2018, Asuka runs away, and Shinji and Misato are worried because she is on the brink of committing suicide.
In a chapter Asuka tells she does not want to have children. That chapter was written after another one where she has just given birth.
Green Tea Rescue begins what appears to be ten years into the future. Izuku and Ochako are a married couple, they share the spot of Japan's #1 hero, have adopted Eri on top of a presumedly biological son. The rest of the fanfic is Eri telling her little brother how Izuku and Ochako met each other, fell in love, and went to become such great heroes.
We are aware from the get-go that the instance of SBURB played in Guidestuck is doomed to fail, and that the characters will all die.
To anyone familiar with Touhou Project canon will know that Yukari's invasion of the moon in Hifuu Club Activity Record ~The Sealed Esoteric History~ will end in a complete failure due to its nature as a prequel fic.
It's (Not) Your Fault: Due to the nature of this comic being an explanation story for much of Javi's art, combined with us seeing the present during the opening, multiple things are certain to happen. Luna and Sam's relationship will not last. Something horrible is going to happen that causes Luna to break away from her family, and Sam and Lincoln are going to end up having Lina by some means.
Lucy's Birth features a five-year-old Lynn and a three-year-old Lincoln nearly drowning, and a baby Lucy almost dying after a hard (premature) birth. However, anyone who's seen The Loud House knows that Lynn, Lincoln, and Lucy all survive.
The Lunar Rebellion: As a prequel to The Life and Times of a Winning Pony, and moreover as an in-universe memoir by Shadow Kicker, it is clear from the first chapter that Shadow and Midnight will survive the war, that the Kickers will remain loyal to the crown, that the royalists will defeat the rebels, and that the clans of Pegasopolis (except the Kickers) will be disbanded. The story is about how those things happened, and the tension comes from not knowing the fates of other characters.
In Neither a Bird nor a Plane, it's Deku!, Izuku Midoriya still says that he becomes the world's greatest Hero. The twist is that he's not the holder of One For All nor does he take up Deku as his Hero Name. He's doing it as the Kryptonian named Superman. Similarly, the author has stated upfront that Mirio Togata is destined to inherit One For All, but has not disclosed how it will happen or when this will take place.
The first flashback arc. We know that Jason and Cass will survive those events, that Lady Shiva will die during them and that Alfred will die one year after them. Everything else is fair game.
The second flashback arc. We know that every member of the Bat-Family will survive the arc and that Dick's decision to retire the Robin mantle will ultimately not take when Jason is forced to revive the mantle during his tenure as Batman. We also know that something will happen that will cause Dick to choose Jason over Tim as his successor, and make Tim amenable and even supportive of that choice.
In the WWE fanfic One More Time, Eddie Guerrero and Molly Holly go on a dessert date. They talk about Eddie's recent health and that maybe he should see a doctor. As the story takes place the night before Eddie died, we all know it doesn't end well.
Pokémon Story: Sinnoh Journey: Obviously, Dawn has her own canon story where she gains five ribbons. Her loss against Aaron is predetermined from the start. That said, the enjoyment comes in the form of character interactions and deeper emotional developments that make it all worth a read.
On the flip side, Aaron being pitted against May in the Wallace Cup ensures he won't be bending canon and winning in that tournament. Other than his two off-screen losses to Zoey, it's the only time in the short story he's shown losing. And rather handily at that.
Similarly, although this story lets Ash go to the Sinnoh League finals (as opposed to the semifinals), he isn't supposed to win. Naturally, Aaron takes that honor from him.
Ian and Aaron only make it as far as the quarterfinals of the Sinnoh Grand Festival, having battled Nando and Zoey respectively. Although, their matches were off-screen.
Sixes and Sevens introduces King Azzuri, the Black Panther of 1943, who is seemingly willing to be less isolationist than previous Wakandan rulers due to World War II encroaching on the country's borders. Though he does give Michael Carter the sample of the heart-shaped herb required for Britain's super-soldier serum, he also stresses that any further attempts to steal from Wakanda will be met with the same violence they doled out to HYDRA and other raiders, and that any further cooperation must come from negotiation and respect. Considering that Wakanda is just as closed-off in Black Panther, it's clear that in the ensuing years no colonial governments will be willing to show such respect after all.
In Sonic the Hedgehog, Maria was a dying Sickly And Delicate girl who ended up shot in an incident. In the oneshot Snow Angel, Shadow and Maria both escape and make it down to Earth...However, being on Earth doesn't magically cure Maria's NIDS. Maria ends up using the last of her medicine within a few weeks and she still dies, just not as soon or as violently as she did in canon.
To Hell and Back (Arrowverse): As per canon, Sam will become Reign one day. The author does not deny it, and it even factored in her decision to not make Kara and Sam a couple.
All This Sh*t is Twice as Weird is an Alternate Universe Fic which (mostly) follows the plot of Dragon Age: Inquisition. It's pretty much confirmed by the premise that the co-Inquisitors will succeed in their long-term goal of defeating the Elder One. What's not clear is why there are two Inquisitors instead of just one, and what effect that will have on the way the story unfolds.
The prologue of The Tyrant and the Hero shows that Heinrich and Black Alice become a hero and the Monster Lord, respectively, and that they're in love. The rest of the story is about how they get here.
From the Robotech fanfic Valkyrie Nights, which is a prequel fanfic to the Macross saga, we know that Roy Fokker survives the events of the story and is cleared of murder charges.
The Very Secret Diary takes place during Harry Potter and the Chamber of Secrets, and shows the off-screen "friendship" Ginny had with Tom Riddle. If you've read the book, you know Tom will eventually possess Ginny and use her to start attacking students, before taking her into the Chamber of Secrets. The fic details how they got there, and it is brutal. It's very well-written and comes highly recommended, but it really is like watching a train wreck.
In Who Decides, the prequel to Horseshoes and Hand Grenades, Ryusei is requesting for help in trying to save Jiro. Anyone who watched Fourze knows that Ryusei will make a Deal with the Devil with the Aries Zodiarts and end up killing Gentaro, thus setting the entire story in motion.
In-narrative example in Z To A; when the time comes, everyone involved is in agreement that Peter Parker and Wanda Maximoff will be the co-leaders of the next generation of Avengers (which currently includes them, Harley Keener, Yelena Belova, and Kate Bishop), with Wanda only surprised that she's included considering her own past mistakes.