Of note is that the film takes place in New York, which either retcons the events in An American Tail: Fievel Goes West (in which the Mousekewitz family leaves New York), or just means that it takes place before said movie. This is addressed directly near the beginning of the film, when Fievel says he had a dream where he moved west.
The film itself involves Fievel and his friend Tony happening upon an encoded treasure map while exploring a subway station. When they bring it to an archaeologist, he concludes that it was written by Native American mice who lived among the Lenape tribe before European mice arrived. He organizes an expedition with Fievel, Tony, a shady rat named Scuttlebutt, and Fievel's feline friend Tiger to explore the tunnels beneath New York, whereupon they find the remnants of the Lenape mouse tribe living in an underground village, where they were forced to flee some 200 years earlier when the Europeans arrived. Fievel befriends The Chief's Daughter, Cholena, and convinces her father to let them bring her to the surface to show her that European mice have become more tolerant. Scuttlebutt informs the evil factory owners (that Fievel's father now works for), who also collude with the corrupt police force, of the expedition's findings. The villains decide they want to invade the Lenape settlement to steal their supposed treasure for themselves. The film begins to take a darker turn as the factory owners whip their workers into a racist panic over the presence of subterranean Native American mice beneath their feet, and an angry mob goes on the hunt for Cholena.
Provides examples of:
- Abhorrent Admirer: As they reach the native village, Scuttlebutt becomes the target of an amorous, huge female mouse. Later said mouse finds out that he's a bad guy and promptly kick his ass.
- Ambiguous Situation: The infamous line where Fievel mentions a dream about becoming a gunslinger can either indicate that Fievel Goes West was All Just a Dream and didn't really happen, or that this younger Fievel is simply Dreaming of Things to Come.
- Anywhere but Their Lips: Cholena makes it pretty clear that she doesn't share Tony's attraction to her, but by the end of the movie she cuts him some slack and gives him a kiss on the cheek.
- Art Shift: Inverted somewhat, as the artists at Universal went back to Don Bluth's character designs in the third movie, but with a few differences, as the designs look like something in the veins of Animaniacs. The fourth movie mostly kept the same designs, but with less shading and more fluidity from the characters. If you prefer the animation of Don Bluth or Amblimation though, you may not like it much. They're still both miles ahead of the animation in Fievel's American Tails (handled by Wang Film Productions and Bardel Entertainment), luckily.
- Award-Bait Song: "Anywhere in Your Dreams"
, sung by Cholena and Fievel, which may also act as a Ship Tease between the two. - Bad Cop/Incompetent Cop: Played straight.
- Beneath the Earth: The subterranean tribe of Native American mice live here.
- Bittersweet Ending: The ending of The Treasure of Manhattan Island is the only Bittersweet Ending in the series. Yes, the evil factory owners who've been exploiting the workers are put under control by Papa's labor union, but they haven't really been defeated, and they haven't really paid for all of the trouble they've caused either. And Cholena's Native American tribe still has to live underground because the European mice are still evil, racist and unable to co-exist with them.
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Broken Aesop: The film frequently comments on the racist treatment of Native Americans and immigrants, with its major theme revolving around breaking down barriers and tolerating other cultures. Despite this, one of the main antagonists, Chief McBrusque, is not only an exaggerated Irish caricature, but is also portrayed as a sinister Dirty Cop who gladly enforces the persecution of these other minorities, despite Irish immigrants actually facing similar discrimination in America at this time. In the climax, Tony even refers to McBrusque as "Potato for Brains" and isn't called out for it, despite similar disparaging remarks about the Natives being criticised. - Broken Heel: Fievel gets his shirt caught on a rusty nail as he and Tony are fleeing a speeding train in the third movie.
- Bullet Seed: Fievel uses this against cops during the climax when they invade the underground village.
- Butt-Monkey: Scuttlebutt, who's frequently mocked and humiliated, has an Abhorrent Admirer and is constantly bullied by the police chief. He even ends up dead!
- The Cameo: Fievel and his friends are shown riding on Henri the pigeon from the first film for a few seconds during a montage.
- The Chief's Daughter: Cholena is this, with most of the side effects; she is attractive yet exotic by Western standards, has a sweet personality, and automatically gravitates toward the European outsiders, albeit without any of the romantic elements this trope usually entails (though her heartfelt duet with Fievel comes close, and Tony is definitely interested in her).
- Chuck Cunningham Syndrome: Bridget from the first movie gets this in the direct to video sequels.
- Continuity Nod: Fievel reminds Papa why they came to America from Russia at the beginning of the third movie, and Mama still hasn't let Papa forget about being wrong when he said there were no cats in America.
- Corrupt Corporate Executive: All three of the corrupt factory owners.
- Crowd Song: "We Live in Manhattan", the song which opens the film and features the mouse residents of Manhattan singing about how much they love living there. Very jarring to viewers who expected the film to take place in Green River.
- Darker and Edgier: This film has themes of racism and politics, making it more on par with the original than the Lighter and Softer tone of Fievel Goes West. It also features police brutality in a scene where the police mice beat up a factory worker mouse.
- Death Course: Fievel and his friends pass through a Death Course while exploring underground caverns on their way to the hideout of an underground tribe of Native American mice. Later on in the film some corrupt policemen are tricked into going through the death course themselves. There are noticeably fewer of them after they come out the other side.
- Demoted to Extra: Tanya, who is reduced to a supporting character, never to shine again.
- Dirty Cop: Chief McBrusque and his police force are in the pocket of the factory owners and gladly carry out their dirty work, particularly when it comes to silencing their enemies. At one point, when Fievel explains what the police are to Cholena, she assumes that the law-keepers will help them, only for Mama Mousekewitz to respond with a Blunt "No".
- Discontinuity Nod: Given the fact that they said Fievel Goes West was a dream in the third movie, Tiger hissing at the angry mob of mice and then accidentally yelling "Woof! Woof!", correcting himself by going "Oops, wrong species!" could also be interpreted as a Take That! (he spends most of that film training to be more like a dog).
- Disney Death: Fievel has one after the tunnels collapse.
- Disney Villain Death: Scuttlebutt and Chief McBrusque actually die, by falling into a deep underground chasm and being drowned by a flood of water.
- Duet Bonding: Fievel and Cholena do this while singing "Anywhere in Your Dreams".
- Edible Ammunition: The underground Native Americans fend of the NYPD with nothing but berries and seeds. Though it helps that, being mice, these police are not armed with guns.
- Fruit Cart: Tony grabs Fievel's hat and playfully runs away with it during the opening music number, before crashing into a fruit cart, bringing the song to an abrupt end.
- Injun Country: It qualifies, though an attempt is made to treat the native mice with respect, unlike the previous An American Tail film.
- Hated by All: The Factory owners are disliked by the mice of Manhattan, due to their greed and corruption, and their refusal to give decent treatment and pay to their workers. Once Papa is able to rally the citizens together and make them see the three Factory Owners are the real enemy, not the Indians, they form a worker's union under Papa’s leadership, and got on strike that is so bad they are forced negotiate with their workers.
- Interquel: If you interpret Fievel's gunslinger dream as Dreaming of Things to Come, then Treasure Of Manhattan Island takes place before the events of Fievel Goes West, with the Mousekewitz family still living in New York. Supporting this is the fact that the film uses the younger characters designs from the original film, rather than the older ones from the second.
- In the Local Tongue: Cholena gives Tony (who'd been hitting on her) the nickname "Poolaook", which he is later disappointed to find out means "turkey". The creators have Shown Their Work, as this actually is the Lenape word for turkey.
- I Warned You: Scuttlebutt does this to Chief McBrusque when he doesn't listen to his warning about the room filled with booby traps.Scuttlebutt: Told you it was dangerous, but did anyone listen? Nooo. Might as well been talking to a brick wall!
- Karma Houdini: Though their plans are foiled and it’s shown they have lost a lot of their employees' respect, the villainous cheese factory owners haven't lost their positions by the end of the film, and don't even get Put on a Bus like most An American Tail villains do. Though their lackeys Scuttlebutt and McBrusque avert this and become the only An American Tail villains to be Killed Off for Real.
- Karma Houdini Warranty: It is implied in Mystery Of the Night Monster that they finally got arrested.
- Little Miss Snarker: Tanya, in a new take on her character.
- Minority Police Officer: The Dirty Cop leading the police, Chief McBrusque, is clearly an Irish immigrant, but has no qualms abusing his power and threatening other foreign mice on behalf of the factory owners.
- Mistaken for Afterlife: Fievel and Tony fall into a deep tunnel when the ground caves in beneath them, and Tony thinks they're dead because he sees a tunnel of light ahead of him (the hole they fell through).
- Pep-Talk Song: "Anywhere in Your Dreams", where Cholena cheers Fievel when he feels guilty over what the Europeans did to her family and that he can do anything.
- Police Brutality: In quite a daring move for a G-rated direct to video movie, The Treasure of Manhattan Island features a police force who savagely beat down protesting factory workers with their clubs, are being paid under the table by corrupt factory owners, and deliberately start a race riot. You know, for kids!
- Politically Incorrect Villain: The three factory owners, particularly Mr. Grasping, have an intense disdain for the poorer mice they employ, especially the foreign immigrants among them, and force them to work long hours with little pay while making themselves rich off their labour. When they learn about the tribe of Native mice living below the city, one of which is now walking out in the open with the Mousekewitz family, the owners then decide to provoke their workers into hunting them down and exterminating them.
- Pragmatic Villainy: When the factory owners are unable to quell their protesting employees, they use the Lanape mice as a scapegoat to turn the workers on them instead. When it's pointed out that the resulting race riot would result in heavy losses for the workers as well as the Natives, Mr. Toplofty reasons that the majority of casualties will be the more passionate protesters, thus eliminating two threats at the same time.
- Retcon: Fievel apparently dreamed the entirety of Fievel Goes West (unless it's just some sort of Shout-Out or Foreshadowing, as Fanon followers usually argue).
- Running Gag: After every time Tanya makes a snarky comment:Everyone: Tanya! Don't help!
- Screw This, I'm Outta Here: When the Native mice start attacking them with fruits and seeds, the police make a hasty retreat.Chief McBrusque: (seeing his men running away) Where do you think you're going?Police Mice: HOME!
- Shadow Discretion Shot: When Chief McBrusque and his officers brutally beat a protesting worker with their clubs, the attack itself is not directly shown onscreen, and is only depicted through their silhouettes cast on the wall.
- Shaming the Mob: Papa manages to stop the riot by doing this.
- Stalker with a Crush: The large native mouse who falls for Scuttlebutt and follows him giggling in an empty tent... just in time to catch him stealing. However this is a Played for Laughs aversion.
- Stay in the Kitchen: Addressed directly. Mama and Papa agree to let Fievel go on the treasure-hunting expedition, but when Tanya wants to go they flat-out refuse. Tanya then complains that her brother always gets to go on adventures while she's stuck at home doing laundry.
- Too Important to Walk: The three factory owners, who get carried around on a sofa by their servants.
- Torches and Pitchforks: An angry mob led by Chief McBrusque hunts down Cholena after being convinced that her being a Native American makes her a threat.
- The Ugly Guy's Hot Daughter: Cholena, who is absolutely dwarfed by her father and looks nothing like him.
- Uncertain Doom: The unlucky protester that McBrusque beats is last shown lying motionless on the ground. Whether he's dead or merely unconscious is not revealed.
- Villain Song: "Friends of the Working Mouse", performed by the three factory owners as they plot to turn their rebelling workers against the Natives and make themselves look like the heroes.
- Wainscot Society: The underground Lenape tribe basically is one. They are able to return to the surface, even after their main tunnel is bombed, through secret entrances.
- Waking Up Elsewhere: Tony wonders if he's dead after he and Fievel awaken staring up at the pit they fell through, after narrowly avoiding being run over by a subway train and falling into an underground cave.
- Wham Line: "I dreamed we moved out west and I became a famous gunslinger!" The line that broke a base, or at least caused many to disregard the DTV sequels entirely.
- What Could Possibly Go Wrong?: Cited nearly word for word by Fievel when he persuades an Indian Chief to let his daughter live among the Europeans for a time and see if they've changed their ways. Things later go horribly wrong.
- What Happened to the Mouse?: A very literal example. After being Demoted to Extra in Fievel Goes West, Tony returns to being a major character in this film. But Bridget, his girlfriend and later wife in the first two films, is completely absent without mention, and Tony is given a new Love Interest with Cholena.
- White Man's Burden: Played straight, when Fievel becomes disillusioned and severely guilt-tripped upon learning what the Europeans had done to the Native Americans, and he takes it upon himself to demonstrate that the European mice aren't so bad...which really doesn't work.
- Worthless Treasure Twist: Worthless to the European mice, anyway. The physical "treasure", as it turns out, is a beaded tapestry that tells the history of the Lenape mouse tribe. The real treasure is the history and culture of the tribe itself. This comes as a disappointment to Tony, who was hoping to get rich, as well as to the villains who wanted to steal it.
