Red's arrivals at the Pokemon Center after the blackouts at Giovanni's battles could be seen as Giovanni giving the poor kid a shred of mercy.
This writeup of the Silph Co. events.
Red stood face to face with the evil Giovanni... All of his Pokémon were weak or fainted... The boss of Team Rocket smirked. "So, little boy... Looks like your Pidgeot only has one move left before it succumbs to poison... What do you hope to do now?" Red smiled. He reached in his bag... and took out the Poké Flute. He whistled a jaunty little tune on it, soothing the Pidgeot's final spasms as the poison took his final ounce of strength. It was okay now. They would go to the Pokémon Center and try again.
Even though the Pokémon may realize how unstable their trainer is, they still listen to his orders and do what they believe is best for him (even if that means digging out of dungeons all the time).
When a rival Twitch streamer sent his followers to sabotage the mob when trying to get past The Ledge, the usually chaotic chat banded together to overcome the saboteurs and managed to get past The Ledge in half the time it took compared to their first time through. In Anarchy mode.
The Mob has become emotionally attached to Red's Pokemon, praising and encouraging them in fights, and not blaming them when they fall in battle. They also will try their best to avoid situations that can get them released.
Everyone's delight at capturing Zapdos.
The fact that TPP has defeated every Gym Leader and captured one legendary, and are still making progress. Make jokes about "start9", throwing away important items, and releasing Pokémon by accident if you must, but when faced with a challenge, the fans WILL band together to overcome practically ANY obstacle.
The memorial posts mourning Cabbage, Dux, and Digrat.
The mob's gradual re-acceptance of Flareon in the wake of Bloody Sunday, including turning his nickname from "The False Prophet" to "The Martyr".
After Lord Helix's resurrection, the mob immediately attempts to retrieve itfrom the PC, despite the fact that they already have a pretty decent team and that the PC taketh more than it giveth.
The Keeper was deposited into the PC in order to clear room for Omanyte. Some have interpreted this (likely final) deposit as Helix ordering his servant to watch over the few remaining Pokemon in the PC and protect them from Bill.
The fact that Operation Shoot For The Moon worked.
Sometimes Red will look to the Lift Key for guidance. If Giovanni really did show him mercy by letting Red go during his battles with the kid, he just might be thinking of those moments.
Before he went to take on Giovanni at Viridian Gym, Red talked to his mom, who healed his Pokemon.
Red defeated Giovanni with Pidgeot.
Everyone rejoicing after his defeat and praising Pidgeot.
Red has all eight badges. The Mob worked together and got all eight badges.
And the Mob has cooperated under Anarchy Mode to the point where Red defeated all 4 Elite Four members, reaching the final Champion battle at least once.
Red let Blue win a Route 22 fight, albeit so he didn't have to navigate a ledge to heal.
During the first fight with Lance, Red was down to only the Level 36 ATV against Lance's much stronger Dragonite. ATV won, causing the chat to declare him a Dragonslayer and worth his place on the team. This is especially heartwarming because ATV was considered the "forgotten" member of the team; that single act alone raised him up in everyone's eyes.
This comic depicts Flareon's devotion to Red, even despite Flareon's absence from Red's party.
This sequel to a fanfic featured on the Tear Jerker page. Everyone is back! Red, recovering from his ordeal, apologizes for what he has put them through, clearly traumatized and crying his heart out like the innocent child he is... but yet the Pokèmon are just happy to see their trainer again, even Flareon, and Pidgeot and company are overjoyed to see their trainer sane and free from his suffering. Notably, this story takes a much more down-to-Earth interpretation, where the Pokèmon are not gods, (note the use of "Pidgeot", not "Bird Jesus", above) but relatively normal Pokèmon who simply love and care for their young trainer, not because of some prophecy or holy plan, but what the Pokèmon franchise is founded on; the mutual love between trainer and Pokèmon.
This comic of ATV going into battle against Lance's Dragonite. If you don't know what "undying loyalty" means before reading it, you certainly will afterwards.