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Tear Jerker: Chaotic
Reggie's backstory's pretty depressing when you think about it. First, he loses contact with his Chaotic self (no doubt making Reggie think he might have been coded permanently). Then, a short while later he ends up in a wheelchair. I know the kid said he didn't mind lossing his legs so long as he found his Chaotic self, but still...
Hoton's entire backstory as told in the episode "Allmageddon". It may even be worse for those who've played the game and already know it. Since the show gives his story much more detail. Not to mention Hoton himself, he just walks back and forth (very slowly) replaceing brick after brick, barley getting anything accomplished, but he never stops trying.
The look of horror on Kaz's face in "Chaor's Commando's" when he sees all three of his friends standing on the very wall that Chaor is about to destroy. Thankfully, Tom, Sarah and Peyton were unhurt.
H’earring falling under Milla’inn’s Mind Control after leading Kaz to where Milla’inn was last seen in "Mister E".
Kaz's mother and the school psychologist taking away Kaz's scanner in "Earth to Kaz". You could tell he wasn't just depressed, he was in real despair for the majority of the episode. His mother even noticed his grades slip dramaticaly, not to mention he'd stopped eating and sleeping. He only got better once she caved in and told the pyschologist to end his investigation.
When Peyton sees what appears to be Sarah getting coded in Perim near the beginning of "Warriors of Eternity". Peyton's horrified reaction is no doubt similar to that of the audience.
Tom and the others being forced to do nothing but sit back and watch as Bat'ogg destroys Perim. It doesn't hit you until later but they've had so many adventures and made so many friends in Perim that it must be killing them to have to just watch while some unstoppable demon destroys it, especially Tom since most of the time he's able to figure something out to help. Throughout the whole episode he's the one who looks most upset, probably because he's faced with the fact that he can't do anything for once.
The death of Tangath Toborn. Or rather, deaths. The first one was shocking enough, albeit an amazing Heroic Sacrifice and Crowning Moment Of Awesome rolled into one, but at that point you could assume he would eventually be freed from the ice, or that even if he had died he wouldn't be gone long. Cue the most recent episode, where not only is his sword broken to enable him to defeat the Big Bad (thus guaranteeing he can never come back to Perim lest he fade away into nothing), we are then treated to several heart-wrenching minutes in which he gets to say goodbye to his closest and oldest friend among the Overworlders, shares a long meaningful look with the human he was closest to, and then gets to dissolve into light, heading off to the Spiritland where "an old warrior like him can live to fight another day". Add in the final very moving memorial service and the monument raised in his honor, and... * sob* So the whole thing was a stupid Retcon the writers threw in without any previous foreshadowing. It still qualifies as an incredible Tear Jerker just because it puts the nails in the coffin, saying "He's dead and won't ever be coming back". (Not unless somehow the kids find a way and a reason to go to the Spiritland themselves.)
Maxxor: He saved Perim not once, but twice...always giving of himself far, far more than we ever could have asked. And so we gather, friend and foe alike, to remember and honor Tangath Toborn, whose struggle and triumph allow us to be here today. Though he has returned to his home in the Spiritlands, we can be certain that his spirit will eternally remain with us here in Perim. And so, on behalf of our generation, and all generations to come, I dedicate this monument: may it stand forever to remind us of a true warrior, a true hero...and a true friend. Farewell, friend.
Najarin and Afjak. Knowing that Tom befriended Najarin thousands of years ago, and accidentally caused Afjak to try to impress his father by leaping into the timestream. Afjak hasn't been seen since. And Najarin has been waiting all this time. A bit of Fridge Horror when you realize that the day on Lake Ken-i-Po is the first time in thousands of years that Najarin has seen Tom, and the first thing that Tom does is try to scan Najarin. Ouch.