Wendy's whole adventure in Never Land can amount to Yank the Dog's Chain; her whole life she loved tales of Peter Pan and always wanted to go to Never Land. However from her first moment, she was shot at by Hook and his crew (though they were shooting at Peter), then is shot at once more by the Lost Boys via orders from Tinker Bell. This nearly gets her killed, and she's guilty when Peter banishes Tinkerbell for it. Afterward, she finally gets to meet mermaids, a species she was so excited to meet since the beginning and they basically attack and attempt to drown her, all the while Peter is laughing. Then when she stands up for herself, everyone treats her like she's in the wrong. Next, after saving Tiger Lily the whole gang goes to the Injuns camp where she is trying to have fun, only to be put to work. No wonder she was ready to go home after all that and willing to grow up. Mr. Darling may be a jerk sometimes, but even he didn't treat her that badly.
Wendy's "Your Mother and Mine" song number. Especially when Smee looks at his "Mother" tattoo and starts sobbing. You just wanna hug him.
Smee may not be the only one who misses his mom. While Hook contently listens to Wendy singing, the other pirates are in low spirits.
By the end of the song, John is crying, and Michael wants to see his mother again.
Wendy's reaction when Hook explains that he planted a bomb in the hideout, decorated as a gift from her, and it's powerful enough to blast Peter out of Neverland. She gives a Big "NO!" and she's horrified as Hook counts down the seconds. When it goes off, she's staring in horror at the smoke.
Then Hook gives his Sadistic Choice to Wendy and the boys, either join his crew or walk the plank. Wendy refuses the former, so Hook has her as the first to go. Her goodbyes to the boys are interrupted when a pirate stops Michael from doing so. If you look closely when she's about to Face Death with Dignity, you can see a tear in her eye as she walks to the end of the plank. Fortunately, Peter Pan arrives to save her in the nick of time.
After Tink saves Peter from the bomb, the hideout is in ruins and Peter begs her to hang on, telling her she means more to him than anyone else.
The ending has Mr. Darling, previously a Fantasy-Forbidding Father, looking out the window in awe and how he saw the same ship a long time ago when he was very young.
Hook: He has found himself a... Wendy? And Hook is all alone.
The fact that Wendy and Peter's relationship is more serious here than it is in the animated movie, and their ship is sunk when Wendy decides to return home with her brothers. Where Wendy's crush in the Disney animated film came across as one-sided, here Peter does seem to have romantic feelings for her but denies them. He protects her from the mermaids while seeking their help to find her brothers, and tries to keep her out of the fight with Hook.
Wendy and Peter's dance with the fairies gets a severe case of Mood Whiplash when Peter abruptly says "it's only make believe" (meaning he's trying to say they're only pretending to be a couple and not really in love). Wendy tries to cover up by saying "of course" but she's clearly devastated.
The following part with their argument is just as sad. Peter won't accept and admit his romantic feelings towards her, and she likewise won't put up with his attempts to deny they even existed.
Peter: Go away and grow up! And take your feelings with you!
Tinkerbell's Disney Death. Everyone knows she'll be alright but that doesn't make Jeremy Sumpter's anguished "Tink!" any less sad.
When the Darlings return home, Mary wakes up and simply walks out of the room. The narration explains that she had so many dreams about the children returning, that she initially thought this was just another one of them. It shows how utterly heartbroken she is over the children disappearing.
The inherent Fridge Horror of the effect the children running off to Neverland in the story is definitely not glossed over in this film. It's quite clear how devastated George and Mary are, implying that Mary is constantly waiting at the window hoping for them to return.
And when Peter closes the window, she frantically wakes up and tries to open it. She's terrified of the children returning, finding the window closed and thinking she and George have forgotten them.
If you know the book, that's exactly what happened to Peter himself. It probably stings him to know that the Darlings desperately don't want to forget their children - when his own mother eventually moved on.
Hook's way of breaking Peter? Telling him a story about Wendy growing up and marrying someone else, keeping the window locked and never thinking of him again. Peter's desperate "I'll call out her name!" is heart breaking. It's also quite reminiscent of what actually does happen in the future, but Wendy does ensure that no one forgets Peter anyway.
The movie's alternate ending shows that Wendy is telling the story to her daughter Jane, who goes to Neverland herself... which drags Peter and Wendy's relationship issues out into the open.
From Peter's perspective: finding out that Wendy did indeed move on from her love with him and married another would've felt like the moment when he came home and found that his mother had replaced him with another child all over again; moreover it would've been a severe blow to realize that, in a way, Hook had been right about his predictions for Wendy. It also would've felt like she'd forgotten about him, and being forgotten is Peter's single most prominent fear. The book takes this moment a step further by mentioning that the moment Wendy began to reach for the light was the single most terrifying moment in Peter's life and mentions that he begs her not to do it.
From Wendy's perspective: Jane asks her mother is she ever minded the fact that she didn't see Peter again, and Wendy replies with "No." This is despite the fact that Wendy continued to wear Peter's 'kiss' around her throat her whole life, as it's pretty clear that the movie was trying to establish the fact that the love between Wendy and Peter was a doomed case of True Love.
And then Peter's utterly empty expression while he's lying on the deck of the ship after being thrown down by Hook is so hard to look at. The boy looks like he's just had every last hope stolen from him.
Hook's death is surprisingly sad. He slowly sinks to his doom while the children chant "Old! Alone! Done for!" He struggles to escape the crocodile, but eventually gives up and resigns himself to his fate.
"You die alone and unloved. Just like me."
At the end with Aunt Millicent. "Then I... am your mother".
Mr. Darling trying to contain his immense relief that his children are okay in the end and tries to act formal, only shaking John's hand... which backfires in them hugging each other in tears.
Peter watching this, hidden, from the window.
Narrator: Peter Pan had countless joys that other children can never know, but he was looking at the one joy from which he must be forever barred.