Clouded Sky

"The truths upon which Tobias's life was founded are shattered, leaving him stranded in a strange, dangerous world. Soon he can no longer tell whether his enemy lies in the ones who hunt him or within himself. After all, evil is in the eye of the beholder."

—Official Description

Clouded Sky is a Pokémon Fan Fiction by Negrek.

Clouded Sky is set in a region known as Waytar, which is believed to be the last remnant of human civilization in a desolated world. An eleven-year-old Farm Boy named Tobias Talltree sets out from his home of Firstseed as a Pokémon Guide, aiming to become a Master Guide, after receiving a Murkrow as his starter Pokémon, which is interpreted by many as an ill omen. However, Tobias soon learns that the world is a much darker and more dangerous place than he ever imagined as his adventure forces him to question fundamental truths about the world that he lives in.

It's hard to say much more without spoiling anything, but it has a very well written and mind-blowingly twisty plot that makes it an incredibly fascinating read.

Tropes used in Clouded Sky include:

Action Girl: Accemenla, Tobias' Tarsix (an original Pokémon species native to Waytar) and the only female Pokémon on his team, can be quite the badass in a fight.
Action Survivor: Tobias is this to a T. He's just an ordinary kid who is constantly being forced into one life-threatening situation after the other through no fault of his own, and continuing to come out of them all unscathed through sheer dumb luck.
Alliterative Name: Tobias Talltree, Damien Darksand
Apocalypse How: The world outside of Waytar's Shield seems to have suffered a Class 3 or 4. Or so we think.
Blood Knight: Accemenla enjoys fighting quite a bit. At times, Tobias keeps her in line simply by threatening to not use her in battles.
Chekhov's Gunman: The story is quite fond of these. One particularly noteworthy example is Marcus Deepriver, who at first appears to be a throwaway extra character only to re-appear after thirty-three chapters as an acolyte at the Water Temple who causes serious trouble for Tobias when he recognizes him from his hometown.
Color-Coded Elements: People who reside in the temples in Waytar wear colors that correspond to their temple based on the Pokémon type that it represents. (Fire Temple = Red, Water Temple = Blue, etc.)
Dark Fic: Compared to the games and show, the battles in this story are portrayed much more realistically, with plenty of blood and the occasional gore. The story can also get very dark, including things such as an oppressive government, murder, and discrimination.
Dark Is Not Evil: Tobias' starter Pokémon is a dark-type.
- All of the other "darklings" shown throughout the story (namely Alex and all of the people who reside in the Dark Temple) are generally shown as being nice, friendly people despite their dark-type affinity.
Deadpan Snarker: Accemenla
Face Heel Turn: Accemenla in Chapter 37.
Family-Unfriendly Death: Quite a few towards the end of the Lighthouse Challenge arc. Namely, George, Cass, Jenny, and Chris, who are crushed by a falling light, dropped through a hole in the floor onto solid rock on the floor below, shot in the head, and blown up, respectively.
Fantastic Racism: Guides who receive dark-type starter Pokémon, known as "darklings", are greatly discriminated against in Waytar.
Farm Boy: Tobias, prior to becoming a Guide.
Frame-Up: At one point, Tobias is framed for stealing and abusing another Guide's Pokémon, forcing him to escape and become a wanted fugitive.
Government Conspiracy: The government of Waytar doesn't want anybody to know the truth about what's really beyond Waytar's Shield and are willing to use some underhanded methods to keep the secret from getting out. Unfortunately for Tobias, they see him as a threat to that.
Hold Your Hippogriffs: Words and phrases based on real-life animals are occasionally replaced with those animals' Pokémon counterparts. This particular line from Chapter 7 stands out.

Alex returned the look with a Mareepish grin, then drew in a deep breath, taking a moment to collect his thoughts.

Loveable Rogue: Alex
Meaningful Name: Lampshaded in Chapter 1 with Tobias' classmate Marcus Deepriver, who, to nobody's surprise, receives a water-type starter. There's also an intentional in-universe example with Jinx, Tobias' Murkrow, since in Waytar, Murkrows are interpreted as bad omens.
- There is also the Slipstri, Alsokaran, which, according to the author, means "Wanderer of Ancient Oceans."
Not So Stoic: This occurs with Igneous, the protagonist's normally very stoic Magmar. During a Pokémon battle, an enemy Girafarig forces him to accidentally injure one of his allies and, due to his constant fear of unintentionally hurting those close to him, he flies into a rage and starts mercilessly pummeling Girafarig, completely ignoring his trainer's commands.
Older Than They Look: Many of the people in the Dark Temple, due to Darklings aging slower than normal people.
One Steve Limit: Averted with Marie the Johtoan trainer and Marie the Dark Temple resident, but otherwise played straight.
Posthumous Character: Waytar's founder, Mayan Waytar.
Puppet King: The master of the Psychic temple and, by extension, leader of the Waytaran government, is somewhat of a literal example. The ones who are really in charge are the two Xatu that always stand behind him. They control his actions and decisions without him even realizing it by psychically planting ideas in his head.
Sssssnaketalk: Alsokaran
The Stoic: Igneous
Time Skip: There is a three-year skip shortly after Tobias arrives in Johto.
To Be a Master: Tobias' goal is to become a Master Guide.
What the Hell, Hero?: Tobias gets called out by Accemenla during a "The Reason You Suck" Speech in Chapter 37 for his inconsiderate actions in abandoning the relatively comfortable life he and his Pokémon were leading in Johto to return to Waytar and putting them all in danger without considering how any of the Pokémon would feel about it.
Weakened by the Light: Accemenla, being a nocturnal Pokémon, really doesn't like sunlight.