Even a show about exploring and friendship isn't immune to sad moments.
- Most of the flashbacks in "Grandpa's Drum," where as a child, Nat was sent off to boarding school and had his Native songs taken away from him. A slightly happier one when Grandpa's songs come back to him.
- Nat's childhood is very sadly Truth in Television; as for over a century-up until the mid 1990s-First Nations children in the USA and Canada were taken from their families to live in boarding schools, where they often suffered horrendous abuse, with the end goal being to strip away their cultural identity.
- A similar thing happened in "Seal Dance." Humans Are Bastards sometimes, aren't they?
- Yet another similar thing happened in "Funny Face Competition" when Molly and Tooey discover an outdated book featuring Alaskan natives forced to wear dance regalia and frown in all photos for the book.
- In "Tooey's Hero": Eugene Pike being unable to cross the icy river to deliver a special package to Qyah for the Great Mail Run due to the ice melting. The mail run would've been ruined if Tooey and Molly hadn't picked up the package from Eugene after giving it to them via rope and delivered it for him.
- In "Little Dog Lost": Tooey getting worried about his new husky Anka after she wanders off after an accident with the dog sled on the way home.
- Warming weather almost causing the planned ice sculpting contest in Qyah to be canceled in the "Ice Sculpture" episode. Molly even mentioned that her mom telling her that they had to cancel made her heart hurt.
- In "Welcome Home Balto," Walter, Molly's dad informing that they would have to cancel their trip to a festival honoring Balto the Sled Dog to deliver a statue of Balto due to an incoming blizzard. It would've been a disaster if Molly hadn't suggested that they get there by dog sled with Tooey and his dad Kenji.
- Molly feeling upset when she can't seem to find any event she's good at while practicing for the Native Youth Olympics. Luckily, she walks across the log with ease (which her other friends have trouble doing) which comes in handy with the grease poll balancing event, which no one else could do before. It also comes in handy when she uses it to get to Oscar when one of his shoelaces break.
- Molly's favorite tree, a really tall spruce tree called Big Sulky, getting knocked down during a thunderstorm. In fact, pretty much all of Qyah have fond memories about Big Sulky and are all equally sad to see it destroyed.
- In the one-hour special Molly and the Great One, Trini's mom Joy finally comes home. It's explained that she was serving in the army. However, Joy's leave does not last long, and when Trini finds out, she's utterly heartbroken. She had her heart set on her mom staying in Qyah forever. She crumples up the picture she drew of her family, and runs into her room crying.
- The Season 2 premiere "Molly and Elizabeth" is another Very Special Episode that shows the ugly side of humanity. Molly and Tooey give a tour of Alaska to some tourists, but they say that they don't look 'native' enough, saddening them. They learn about Elizabeth Peratrovich and how Alaska Natives were segregated from white people back in the day.
- In "Gold Strikeout," Molly, Tooey, and Trini try to prospect for gold in 'Gold Creek,' but the sluice box they use ends up blocking the salmon. Nat tells them that the book they read was Written by the Winners and doesn't tell the whole story of what happened. They watch an interview of a woman speaking about how her family was forced off their land by the gold panners. Eventually, the salmon in the creek stopped coming, and members of the native community got very sick.
- In "Wise Raven and Old Crow," the subplot of the special is Trini and Tooey taking care of a baby moose. However, the moose eventually goes missing. Trini goes through another Break the Cutie moment and starts crying, thinking that it's her fault that the moose got lost. It is obvious that she and Tooey are lost without Molly there to guide them.
