Twilight Princess was famously intended to provide the darker take on The Legend of Zelda that fans were hungry for in the wake of The Wind Waker. TP may have taken that darker vibe a bit too far though. After defeating Ganondorf – instead of sealing him away as has been done countless times in the past – Twilight Princess' Link takes things a step further and outright kills the Demon King.
While this deadly outcome is thematicaly and tonally consistent with the rest of Twilight Princess, it has wide reaching consequences for the Zelda series at large. Namely, Ganondorf's death at Link's heands inadvertently forced Nintendo to split the already messy Zelda timeline into three distinct branches. The Fallen timeline wouldn't exist if Nintendo remembered that Ganondorf needed to be alive for A Link to the Past to happen.
A Link to The Past Introduced The Imprisoning War
The Legend of Zelda: A Link to the Past details a period of turmoil prior to the game's events. Ganon sought the Triforce's power and after successfully securing it alongside his group of thieving sorcerers, he assembled an army to help him achieve his selfish aims. Eventually, the King of Hyrule assembled the Seven Sages to lock Ganon away in a magical seal. This entire struggle became known as the Imprisoning War, and set the stage for ALTTP.
Ocarina of Time acts as a prequel to ALTTP and the Imprisoning War, which makes sense given Ganondorf's initial rise to power is detailed in that game. After his rise and defeat by Link, Ganondorf is sealed away as depicted in ALTTP's lore. From there, Ocarina of Time's time travel splits the series' canon into two timelines – one in the future where Adult Link defeats Ganondorf and seals him away before Zelda sends him back, and one in the past where Ganondorf's plans are foiled by Child Link now that he has the Triforce of Courage. Because The Wind Waker followed up the Adult timeline with a story where Hyrule is flooded and therefore the Imprisoning War can't happen, it was up to Twilight Princess to lead into A Link to the Past.
After The Wind Waker was released, Twilight Princess was the Zelda Timeline's last hope for some reasonable clarity. Ganondorf's plan had been foiled, but in order of ALTTP to still make sense, Twilight Princess simply had to let Ganondorf escape captivity and enact his plans anyway. At first glance, Twilight Princess' plot actually does a good job of this, showing how Ganondorf is sealed away in the Twilight Realm after receiving the Triforce's power. This set-up could have still fit into ALTTP, but the Zelda team had other plans with the game's ending. Had Twilight Princess merely ended slightly differently with Ganon only being banished instead of killed, ALTTP could have naturally followed. Instead, Four Swords Adventures had to follow Twilight Princess as Ganondorf needed to be reincarnated instead of unsealed, and thus the Fallen Timeline was born to accommodate ALTTP's preestablished place on the timeline.
Ganondorf's Death in Twilight Princess Caused Most of Zelda's Lore Inconsistencies
While Twilight Princess is viewed by many as one of the definitive 3D Zelda games, its mere existence caused most of the confusion within the Zelda timeline as it stands. That's because TP created the need for the "The Hero Is Defeated" (aka the "Downfall" or "Fallen") timeline. Every game on the Downfall branch could have easily fit on the child timeline in pretty much the exact order they already do, had Twilight Princess not killed off Ganondorf to begin with. The Hero's Shade was the perfect tie-in to solidify Twilight Princess as a sequel to Majora's Mask – all A Link to the Past required of Twilight Princess was to keep Ganondorf alive and sealed away in order to add a bit of consistency to the pre-determined lore.
Whether due to the fact that the Zelda team simply ignored or forgot ALTTP entirely, or because they just wanted to add to that dark atmosphere already established in TP, an irreconcilable split was formed. The main problem with the downfall timeline is that no other game in the entire official timeline has a separate timeline that splits whether the hero wins or loses, so this creates an odd divergence on the entire timeline. OoT's Adult and Child split actually made perfect sense, but in splitting the timeline a third time to account for the hero’s off-screen defeat, things became way more complicated than they needed to be.
Tears of the Kingdom's New "Imprisoning War"
Despite the problems that Twilight Princess and the Downfall Timeline have caused, Zelda's devs seemed to make one last ditch effort to save the timeline in the latest game in the series. Tears of the Kingdom seemingly retconned everything by making the Zonai Rauru not only the first King of Hyrule, but also the root of the Seven Sages' power by means of the Secret Stones. This would make all Sages in the subsequent games (or prior games in real life chronology) descendants of those shown in TOTK. Additionally, this set up the imprisoning war in a completely new way, and showed Ganondorf and his army directly attempting to usurp the throne by means of the power of the gods.
At this point, Breath of the Wild and Tears of the Kingdom may be the only certainty left in the Zelda series' timeline, with every other game at this point being relegated to "myth" according to 2018's behind the scenes book, Creating A Champion. Like most myths in real life, the entire timeline prior to Breath of the Wild is given a kind of leeway for consistency as they're considered stories more than concretely factual moments in time. Events in prior games clearly did happen in some way, as hints to them show up throughout both BOTW and TOTK, but whether they happened in the order the timeline provides or in the exact way as they're "told" through previous games is left up to interpretation. As it says in the fine print below the timeline in the Hyrule Encyclopedia: "the timeline can be interpreted in a number of ways, and may change depending on new discoveries that have come to light and on the players' imaginations." It's certaintly taken a good amount of imagination for players to try to reconcile the inconsistencies Twilight Princess caused.