NOTE: Another great spoiler (number 50-something, I lost count) sent in by Brentage5000.
The movie starts with the legend of a great warrior who nine thousand years ago was poised on the brink of global domination and immortality. This warrior had a massive army assembled and was all set to receive his immortality, but something unexpected happened. When it came, it was through a dimensional portal that not only made him immortal but also brought thirteen monsters with it. As an added bonus, his four greatest generals, who were assisting him with the ceremony, were turned into stone. Legend has it that until nine stars are aligned again, something that only happens every three thousand years, this will be unable to be repeated.
Cut to present day. In Central America, we see a bunch of poor villagers being accused by some local toughs who threaten them and steal all their essential supplies. They take off laughing and start driving through the jungle when they are blocked by a tree in the road. Two of the guys get out to move it, but one of them is puled into the tree tops by a rope and the other is knocked into the shadows by an unseen being. The naive driver starts babbling about a "jungle ghost" and takes off while the leader begins searching for the so-called ghost. He somehow gets backed up against a tree and we see a green beak poke out of the shadows just before--
In the village, the people are walking about when suddenly the bad guys jeep comes back with all their supplies, and a boy sees a cloaked figure in a tree in the distance. Some time later, we see April O'Neil (Sarah Michelle Gellar) talking to the boy, who points out the tree he saw the figure in. April thanks him and heads off, slicing her way through the plants. She tentatively calls out a couple times, looking for someone, when suddenly the ground gives way and she falls through some vines only to be caught by something that says, "It's a long way from the city to come for a visit, isn't it?" She looks and sees Leonardo (James Arnold Taylor), and soon the two are talking over a campfire. Leo asks after his brothers, and we see that they've each moved on. Donatello (Mitchell Whitfield) has started a one-turtle tech-support company, Michaelangelo (Mikey Kelly) has started a party business where he basically puts on a giant fake turtle mask (heh) and calls himself "Cowabunga Carl", and Raphael (Nolan North) apparently does nothing but sleep 24/7, although he secretly dons a metallic outfit at night (think Iron Man....or Iron Turtle, rather....but with no pyrotechnics) and prowls the streets as Nightwatcher, a particularly ruthless vigilante that The Punisher would feel right at home with. We also learn that Leo has been living here for the past year in order to find himself as a leader, and he doesn't want to return lest Splinter think him a failure. April pleads with him to come back, but he vanishes and leaves her talking to air.
Back in New York, we see Mikey's van riding through the streets and pulling into an alleyway. It passes a wall covered with graffiti which lifts up and backs in. We see a manhole falling into place and soon Mikey is rocketing through the pipes on his skateboard before coming to a rest in front of an apparent dead end. He flips a pipe, and a secret wall opens and admits him into the turtles' lair. He tries to make a big deal out of this, but is defeated by the utter lack of anyone there to welcome him. Defeated and deflated, he sits down to watch a story about Nightwatcher as Don comes in and makes some degrading comments about him just as Raph comes in to say at least he (Nightwatcher) is doing something. Splinter (Mako) comes in and stops the argument from escalating, and Raph heads off to bed, leaving Donatello to tell Splinter, "Maybe you should have sent him away."
Meanwhile, over at the docks, April is busy supervising the unloading of some ancient statues for her cargo business. She notices a distinct lack of delivery boy and calls her boyfriend, Casey Jones (Chris Evans, aka the Human Torch in Fantastic 4). She calls their apartment and wakes Casey up, telling him to get his butt down there pronto. Soon, April is leading Casey (who, in turn, is leading a giant crate) into Winters Industrial, the place of business for her client, Max Winters. She tells him to be careful just in time for him to knock over an antique vase, and pretty soon security doors are descending, locking them in (important). Winters (Patrick Stewart) comes down, resets the system, and takes April and Casey up to his office, where they each gaze at the four immense statues inside, and Winters recounts the legend told at the beginning of the film.
That night, Raph is on the rooftops in his Nightwatcher gear and taking care of some criminals when Casey suddenly pops up and lets on that he knows it's really Raph underneath. They finish up the criminals and then talk, and Raph lets out that he does miss Leo a little. Meanwhile, we see Winters in his base planting some devices on the four statues and waking them up. He is interrupted by the remaining members of the Foot Clan, currently under the leadership of a woman named Karai (Ziyi Zhang). He tells her that he will be needing the foot to assist his generals (the statues) to locate and capture thirteen monsters, and after some attitude, she agrees.
Elsewhere, we see a South American plane coming in for a landing in New York, and propped up on the landing gear is Leo. He leaps off and lands in the water, and soon is making his way through the sewers. He enters the Turtles' base and finds an unsurprised Splinter in his dojo. Leo apologizes for failing, and Splinter says that he didn't and has to make his family a team again....so no fighting bad guys, in other words. Leo wakes up Don and Mikey, and they are overjoyed to see him....although when Raph enters, he is considerably less ecstatic than the rest and just goes to bed. Things haven't improved the next morning, when Leo tells them that they're going out for retraining that night, which Raph is naturally against. They meet up at a building in the Bronx and Leo starts to lecture them when they are interrupted by the sounds of a fight at a construction zone. Leo's brothers go to check it out, and Leo reluctantly follows. Once there, they see members of the Foot fighting a huge monster that kinda looks like a Wampa from Star Wars. Mikey at first wants to just watch them get beaten, but eventually they join in. The foot see this and at a word from Kairi (who almost guts Leo when she sees him), they vanish. The turtles keep fighting the monster, and eventually it pounds its way through the floors and hits the ground hard, where it is taken by the stone generals. Meanwhile, the turtles head home, with Mikey giving them a ten for style, an eight for ability....and a two for stealth.
In Winters' private room, he puts the caged monster back in a position around a circular disk, and it's right about now we realize that Winters is the warrior that all those legends speak of. Back with the turtles, they're having breakfast and talking about last night's battle when Splinter enters and they shut up so he can watch his stories ("I wonder if Donna and Carl will finally get together today.") Unfortunately, the minute he turns on the TV he hears a broadcast about the fight last night, and soon the boys are all in his dojo being reprimanded. Meanwhile, we see the generals cleaning up the city of monsters until only three remain, and Winters has each of them put in cages while simultaneously refusing Kairi who asks for more leeway when it comes to getting the monsters. At the same time, the boys are going over some facts and figure if the monsters aren't stopped, the world has about eight months before things are completely ruined.
A few nights later, Casey is watching TV as April practices some moves with her single katana (as opposed to Leo's double set) when Raph sneaks up and beckons him to the roof. He grabs a bat and mask and heads for the roof while April talks about a job offer -- salaried -- she might get from Winters, though when she sees his foot heading up the fire escape, she leans out and whispers, "Be careful." On the roof, Casey and Raph are talking when they hear a fight a few rooftops over. They head for it (don't ask me how Casey was able to keep up) and see the generals battling some sort of bat-monster. They catch it, chop off its wings, and throw it in a cage. As they're watching, Casey accidentally knocks a piece of rooftop loose and two of the generals are soon taking off after them, assisted by some foot clan members. They hide in a rooftop tool shed, but one general manages to get the door open enough for a foot to shoot some tranquilizer in that hits Raph. Before things progress, some cops show up and the generals bolt. Casey breathes a sigh of relief but then sees an unconscious Raph next to him with a piece of the generals' weapon sticking out of his back.
Pretty soon, all the turtles are gathered at April and Casey's apartment, and after examining everything and getting Raph awake, they figure out that their attackers were the generals in that legend and that Winters is behind everything (his name was on the tranquilizer shot at Raph...literally). Leo tries to get the others into it, but Rpah doesn't want any part of it and says, "I quit." A day goes by, and no one hears from Raph. Meanwhile, the generals are beginning to realize that once Winters has all thirteen monsters, their immortality will be forfeit, so they begin laying plans against him. That night, Raph is out as "Nightwatcher" when he sees some chaos happening at a diner. He goes in and calms the babbling head cook (played by Kevin Smith -- WOOT!!!) down and heads into the kitchen, where he gets trounced by the latest monster, a cute little pink devil that would make a great pet if it didn't eat anything that moved. Raph gets it outside but it gets away. He goes to pursue but Leo shows up to put an end to the vigilante's activities (he doesn't know Raph is Nightwatcher). Eventually they end up on a rooftop and Leo tries to reason with "Nightwatcher", but "Nightwatcher" isn't having it and they fight, but the mask gets kicked off and Leo sees who it really is. Raph yells at Leo, with seventeen years worth of anger spilling out, and the two start fighting again. Raph somehow gets the better, breaks Leo's katana, and is in a perfect position to kill him, but he takes off running. Suddenly, the generals show up and knock Leo out, figuring that he's not human, so they can just tell Winters that he's the last demon, and he won't realize the truth until it's too late. Several rooftops away, Raph hears the fight, but is too late getting back and screams, realizing what he's done.
Some time later, Raph heads back home and confesses what he's done to Splinter and apologizes for not being a good son. Splinter responds by saying that while Raph may not be his favorite STUDENT, he is far from his least favorite son. Soon the whole team -- including Casey and April -- are making plans to get Leo back, and April gives Leo a little gift -- an obsidian mask that she got in Japan for him a little while back that won't break as often as his wooden ones. Later, they pull up outside of Winters' tower, and while Casey distracts Kairi with Mikey's mask, April, Splinter, and the other three scale the wall and sneak in. Inside, Winters is starting up the process once again to get rid of his immortality when things start going wrong and as the battle between the foot and the turtles rages outside, the generals tell Winters that they have no plans on becoming mortal again. Finally, Team Turtle gets into the building with Casey breaking another vase to keep the remaining Foot out. They free Leo and Winters tells them what happened just as the generals show up. The turtles and Splinter stay behind to deal with the generals while April, Casey, and Kairi go to find the real thirteenth monster (apparently number twelve, Pinky, got captured while Leo and Raph were fighting). Pretty soon the van is rocketing through the streets with a dragon on its tail as Casey and April argue about Casey's driving (Kairi to the Foot ninja that came with them: "You'd think they'd be more worried about what's behind us."). Casey drives the van through the lobby just as the turtles get all four generals lined up. Casey puts the van in a braking skid and the dragon flies over the van, crashes into the generals, and lands in the vortex, sending both the generals and the monsters to another dimension. As the team pulls itself clear of the rubble, Winters begins laughing joyously, a mortal again. As the turtles watch, a powerful force goes through his body and illuminates him just before he turns into dust which Mikey accidentally breathes in and begins choking on. Meanwhile, Kairi states that it was an honor working with them, and when their leader returns to full health, she will try to kill them quickly and honorably, leaving the turtles to wonder just who she meant when she said leader...
Later, we see Splinter carrying Winters' armor and putting it on a shelf in his dojo. He looks to his left and sees Raph there with his Nightwatcher helmet, and Raph puts the helmet up there too, retiring it from service. Mikey speaks up behind them and says, "Is there room for this up there?" and we see that he is trying to retire his "Cowabunga Carl" mask to the trophy shelf. That night, we see the turtles jumping across the rooftops as Raph reflects on just what it means to be a turtle, what it means to be a hero...and what it means to be family.