Totodile's backstory. Period. Before the events of the story, Taki heard the sounds of sobbing in a misty forest, which were coming from a Totodile. She brought her to the Ho-Ken temple, where Chief Tanaka revealed, after having a brief talk, that Totodile had been abandoned by her trainer. Doubles as Heartwarming when the chief inspired Taki to take in Totodile, as her trainer.
It is later revealed in United Bonds that her old trainer was none other than Simon Varnett
Although she was only present for a small number of chapters, Venusaur's death is bound to bring the waterworks.
Even worse, her death took a huge toll on the main protagonist.
And in the second final chapter, when Louis sees a sketch of him and Venusaur, drawn by Tracey Sketchit, Louis falls onto his knees and cries.
Louis' emotional breakdown in the Lugia Temple. which was a combination of the pressure surrounding the hunt for the crystal shards, and Venusaur's demise. As part of the anger stage of grief, he attacks Team Rocket, but is held back. Taki manages to calm him down, and soon, Louis begins crying into her shoulder.
Pokémon: United Bonds:
Louis' parents, Taki, Crocanaw, and the Ghostly Trio seeing the titular character off for his trip to the National Pokémon Academy. Any parent who has seen their child grow and leave to pursue their dreams is bound to shed a few tears.
Learning about Azul, and his sister's, former trainer. Having been forced to retire from being a Pokémon trainer after being attacked by a Tyranitar during a battle, the trainer sent the two Froakies to the academy so someone else could take care of them.
After learning that Simon was the trainer who abandoned Crocanaw when she was just a Totodile, along with being slightly homesick, the stress begins to take its toll on Louis. Unfortunately, during a spat between the boy's team of Pokémon, Louis snaps at them, letting loose his frustrations, culminating with him believing that being a trainer was a mistake.
Learning about Cubone's mother's death can make just about anyone cry. During a storm in Kanto, The Marowak managed to find shelter and held onto Cubone, to preserve the heat in his body. Cubone survived the storm, but his mother...she never woke up.
Doubles as Heartwarming as Louis gives Cubone some wise words on how to never forget loved ones. This in turn leads to Louis finally accepting Venusaur's death.
Suzuki's graduation and Azul's departure to the Kanto region will likely have tears flowing.
Pokémon: Free Will:
Something happened between the second and third book that drove young Louis to quit being a trainer. He didn't go back to the academy for nearly six years.
It isn't until later in the story that we learn exactly what happened. Louis was about to sign up for another year at the academy until he spotted Azul, who evolved into a Frogadier, sitting by a fountain. The pair reunited, then Azul asked if they could have a sparring match with someone, which they ultimately lost. Azul took it hard and ran away, swearing off battling. This left a bad effect on Louis, as he blamed himself for what happened. His mind began antagonising the boy, ultimately culminating with Louis uttering the fateful words...
Louis: ...I quit.
Louis and Azul's argument after the battle royale. After the Greninja's words left a bad taste in his mouth, Louis confronted him on his choice of words. He simply brushed the trainer off, which led to Louis accusing the Greninja of being a "selfish, arrogant jerk". Louis also accuses Azul of never being for the team from the beginning, and only cared about himself, ending with Louis deciding to cut ties with Azul.
Azul's tearful apology to Louis at the beach. Having learned of the consequences of his actions years ago from the young adult's father, Miguel, the Greninja felt tremendous guilt. So much so, that he broke down sobbing, apologising for his actions.
