Aborted Arc: The side-plot of the Kid getting the throne of the city back literally comes out of left field (we're barely even told anything about how important the kid is; Jak only rolls with it because it means overthrowing Praxis) and barely receives so much as a handwave throughout the game. Then once Praxis steals the Precursor Stone, that's the last we hear of the Kid's inheritance plot thread.
While the kid's importance dries up in the second game, his presence (or lack thereof) is very important to the third game.
Affably Evil: While Jak is working for him, Krew is affable enough, seemingly delighted in Jak's enthusiasm to blow things up for gun mods. But when Jak doesn't play by his rules, Krew becomes angry and threatens him.
Always Chaotic Evil: The Hora-Quan, AKA the Metal Heads, the sworn enemy of the Precursor race and the main threat of the game. Subverted with the Lurkers, especially Brutter, who were this in the first game.
Arbitrary Gun Power: Justified in most examples, since what you're shooting usually has super strong armor.
Attack! Attack... Retreat! Retreat!: Daxter inadvertently activates a handful of Plasmite Grenades, with Vin trying to keep him and Jak calm. Vin: "Don't move! [Beat] On second thought, move! Far away!"
The Atoner: Torn, who was a Krimzon Guard officer, but quit to join the Underground when he discovered how the Baron was more than willing to sacrifice innocent lives and resort to brutal, fascistic tactics in order to keep Haven under his control.
Awesome, but Impractical: The Vulcan Fury can dish out damage fast and is great for attacking large groups of enemies, but is hard to aim and chews up ammo so quickly that it's best used sparingly. The Peace-Maker dishes out a ton of damage, can electrocute targets close to the main target, has very long firing range and a homing ability, and a very fast firing rate—but this is all brought down by it's pathetically low ammo capacity. Also, Dark Jak is powerful (especially its upgrades) but it takes so much Dark Eco to use and lasts for such little time, that it's best used as a last resort.
Broken Angel: Kor, who is normally a giant insect/reptile like Metal Head creature, but is trapped in an elderly, frail human form when he's inside the city, subject to its strong eco-powered shield wall.
Brother Chuck: Brutter the Lurker only appears in this game and Daxter, and isn't even mentioned in Jak 3.
Call Back: In an early mission, Daxter states that retrieving a gear (causing an entire machine to spectacularly collapse) is like taking candy from a baby. He later makes this proclamation when retrieving the Precursor Stone.
Car Fu: Zoomers serve three purposes: transportation, racing and crashing into stuff. Guess which is the more fun thing to do?
Cerebus Syndrome: This game is one of the most famous, beloved examples of Cerebus Syndrome ever done in a video game. It's gotten to the point where some gaming communities refer to this trope as "Jak II Syndrome".
The Dark Jak ability is not only what saves Jak from dying before the final battle against Kor, but can also be used to help turn the tide in the battle, as you can automatically trigger it during the fight once, regardless of eco meter. Keep in mind, outside of the first few minutes of the game, the ability has very little effect on the plot.
The machine at the back of the Hip Hog Heaven Saloon. It contains the Time Map, and on your first playthrough without being spoiled, you'd probably think that it's just there for decoration.
City of Canals: North Town and the Water Slums. The main slums also have large trenches, although the purpose of these isn't clear.
Cool Bike: The Zoomers, both out on the street, and the ones you race in the stadium.
Cool, but Inefficient: The Hellcat cruisers, which look cool, but are only equipped with the same wimpy gun as the Krimzon Guard Zoomers and don't allow you to use the top cannons, not to mention the thing moves as slow as molasses, and it's large size is a huge liability in the claustrophobic streets of Haven City, making it not only very easy to crash and burn, but also serve as target practice for the local guards.
The Corruption: The Baron's announcements insist throughout the game that Jak will slowly lose control of his Dark powers and it will eventually destroy him from within. Talking to the Oracle confirms the Baron's warning. "I sense there is a dark rage burning within you, and in time, it'll destroy you with its madness." Thankfully, Jak learns to control them by the end of the game, and the Precursor that is released from the stone tells him the darkness is now balanced by a glorious light.
Cosmic Egg: The Precursor Stone is actually the last Precursor Egg.
The Dev Team Thinks of Everything: Trying to run too fast through the city before it can load everything up ahead? The Naughty Dog dev team is quite literally one step ahead of you. Upon the game encountering a situation like this, Jak will instantly fall flat on his face and take a few seconds to get back up, giving the game time to load the scenery up ahead. Also, if you try to pass through a security gate by hijacking a vehicle passing midway through, the force field will instantly vaporize you.
Escort Mission: Made even worse by the people you're escorting being utter morons. Ironically, the Kid, who is a toddler, is the least likely to get caught.
Establishing Character Moment: The first thing Jak says to Daxter when Daxter finds him in prison. It's quite a turnaround, breaking his previous role as a Heroic Mime and showing how two years of torture have changed him.
Eyepatch of Power: Praxis has a metal plate covering one of his eyes, a reminder of his failure to breach the Metal Head Nest. Sig has what appears to be either a bionic eye or a fancy lens of some kind.
Fake Difficulty: Sure Jak II's more difficult than the previous game, but a lot of the difficulty comes from really cheap tricks: trial and error gameplay, long sections with plenty of instant deaths but no checkpoints, timed missions with zero room for errors, etc.
Fake Longevity: One could argue that the mission-based structure leads to a lot boring and repetitive driving from one location to another, especially when the hub city is built to be such a maze that the drive distance between those locations is often unnecessarily long.
Fantastic Racism: Haven City is this towards Lurkers, who were the first game's main enemies, now.
Fashionable Asymmetry: Jak's single shoulder pad and triple-strapped backpack come to mind, as well as his goggles (one lens dosen't even appear to be see-through!)
Game-Breaking Bug: There is a notorious glitch where if you don't go to the final bike race immediately before doing any other missions or side-quests, Keira will not appear, making it impossible to complete the game, and thus forcing you to start over completely from scratch.
Ghost Town: Dead Town, a flooded locale made of crumbling, ancient stone buildings right outside Haven's shield walls, the result of Haven's old barrier wall being breached by a Metal Head attack, and the Baron ordering the Krimzon Guard to retreat behind the newly built shield wall, leaving behind the inhabitants to die. Only a young Samos the Sage survived, who used a magic life seed to repel the onslaught.
I'm Dying, Please Take My MacGuffin: Baron Praxis gives Jak the Precursor Stone (albeit hidden inside the backup Piercer Bomb) before he dies from the wounds inflicted by Metal Kor.
Imperial Stormtrooper Marksmanship Academy: The Krimzon Guard, minus Ashelin, are usually lousy shots, but if they can fire off three or four shots in a row without being interrupted, the last one will be unerringly accurate.
Indy Hat Roll: Done in Mar's Tomb, with Daxter serving as the hat.
Invisible Monsters: One mission involves hunting down a bunch of (almost) invisible Metal Heads hiding out in Haven Forest.
Irony: The Baron stating via the propaganda machine that there are no Metal Heads in the city, and that anyone who contradicts this fact will be shot. In the game's climax, he gets killed by an energy blast courtesy of the Metal head leader.
I Will Fight Some More Forever: You'd think the Krimzon Guards would've learned eventually that picking a fight with Jak is comparable to suicide. Nope.
Jerk with a Heart of Gold: Jak eventually develops into this by the end of the game and stops caring about personally getting even with the Baron in favor of just toppling his rule.
Karmic Death: Erol, who is so obsessed with personally killing Jak that he tries to run him down on a Zoomer in front of a huge crowd... only for Jak to dodge, and Erol to crash and burn into a whole bunch of eco barrels.
Knight Templar: Baron Praxis will do anything to make sure the Metal Heads won't win... even if he has to arrange for everyone else to lose.
Lost Forever: The Metal Head Nest cannot be returned to after you beat the Metal Head leader, losing you seven Precursor Orbs and some Metal Head Skull Gems if you didn't take the time to snatch them up. Fortunately, there are 286 Orbs in the entire game, so it's not that big of a loss. The tower in Dead Town is rendered inaccessible due to it collapsing (although it's possible to reach the remaining platforms by using a well timed jump while using Dark Giant). The Drill Platform control tower is also rendered inaccessible after you blow it up late in the game. Also, some people think that the eco mines are inaccessible after the three missions you do there, but the entrance is conveniently located in the warpgate located in the first room you start the game in, right within the fortress! Convienient, huh?
If you are a trophy collector and have gotten the Jak And Daxter HD Collection, the previously mentioned Metal Head nest will make getting the platinum trophy impossible as the trophy requires you to get all 286 orbs. So yeah, Have fun with that. There is a Good Bad Bug that allows you to obtain infinite Precursor Orbs, however, by restarting sidequests while getting the precursor orb required to beat the side quest. However only a few side quests can be exploited and if you beat all of those sidequests AND failed to get all the precursor orbs in missable areas...then you're screwed.
MacGuffin: The Precursor Stone, which has the last Precursor life force hidden inside of it.
MacGuffin Delivery Service: Just when Jak finds the stone, the Baron arrives with a Mini Mecha to steal it. Jak technically wins the battle, but the Baron still gets away with the stone.
Male Gaze: Daxter glances down at Tess' boobs when they meet at the bar. At least he looked her in the face first.
Man Hug: An incredibly drunk Daxter hugs Jak while slurring "I love you, man!", which earns a disturbed look from Jak.
Mecha-Mooks: The ball-bots that roll around bumping into Jak and the smaller spider robots. They make occasional appearances in the weapons factory, the Baron's fortress, and during the second boss fight with Baron Praxis. They later reappear in Jak 3 as more prominent enemies.
Mind Screw: The more you try and piece together every aspect of the games Time Travel plot, the more it hurts. Lampshaded by Daxter, of course. Keira's just finished building a replica of the time machine that brought the group to Haven City, and is worried that she didn't remember it quite right.
Samos: It's perfect, Keira. This is the very machine we found... or, will find, later.
Keira: What? I just built this! After seeing the first one, I mean. It's based on what I remember from—
Daxter: Honey, the more you think about it, the more it hurts the head.
Mineral MacGuffin: Despite its name, the Precursor Stone looks more like a big green jewel.
Mini Mecha: The Baron's two combat mecha, the Krimzon Blast Bots, and the Titan Suit Jak uses late in the game.
Monster Protection Racket: Praxis and the Krimzon Guards do this with the Metal Heads, though it's an unusual variation as in this case the Metal Heads are a genuine threat rather than a hoax.
Mordor: The eternally storm ridden Metal Head Nest, the outskirts of it being littered with the rusty, crumbling remains of a failed attempt by the Baron to attack the nest years ago—specifically, lots of stone walls and towers, lots of old, rotting tanks... and the superweapon Mar built to blast open the nest.
Mythology Gag: The Item Get jingle from the first game pops up at the end of the first mission you get, only to get parodied.
Never Trust a Trailer: One tv promo showed Jak and Daxter being carried off by a Krimzon Guard cruiser in a scene that the trailer made it seem like they were being kidnapped from their world and brought to Haven City. The clip in question was from a part in the game where Jak and Daxter were willingly using the transport to just reach another destination.
New Game Plus: Hero Mode, which is unlocked by getting 200 Precursor Orbs. It beefs up the difficulty of the game, but grants you all four of your guns right off the bat, and makes it easier to get the Dark Jak powers, as the Metal Heads always drop skull gems in this mode. Getting 200 orbs in this mode also rewards you with the Alternate Scrapbook.
Nice Job Breaking It, Hero: Jak is the reason the Metal Heads got into the world in the first place AND got them sent into Haven City, whether he intended it or not. Also, there is tipping off Kor (while human) that the Baron was going to stab him in the back.
Nintendo Hard: Parts of the game fall into this, but Hero Mode takes the cake.
No Kill Like Overkill: Praxis plans to use a bomb that can destroy the universe to blow up the Metal Head nest. Justified as he is unaware of this.
Noodle Incident: Jak to his younger self: "Stay away from ANY wumpbee nests on your ninth birthday, okay?"
No MacGuffin, No Winner: Our heroes do have the stone by the end, but it's rendered useless when The Kid touches it, thus releasing the Precursor Life Force hidden inside of it.
Non-Action Guy: Daxter is still this, but starts to show signs of shedding it, as he actually helps Jak in some parts where he couldn't have done it himself; he is also the gunner when Jak is busy driving. Also, Vin.
No OSHA Compliance: The Fortress, the Weapons Lab, the Eco Mine, the Drill Platform, and the Palace's support towers.
Random Events Plot / Kudzu Plot: Just try and sum up the entire plot, complete with all the threads, subplots, character arcs, time travel logic involved with it and foreshadowing it manages to cram in, and make any sense of it.
Rising Conflict: Jak's original motive is revenge on Baron Praxis for the two years of imprisonment. By the time we reach the Third Act, he's working to save the city from the Metal Head invasion and Baron Praxis is killed by Metal Kor.
Stripperific: Ashelin, the only female Krimzon Guard we see, wears a "uniform" like this.
Stuff Blowing Up: Lots of it in game, especially if you chose to pick a fight with the Krimzon Guards, have a lot of firepower at hand (or maybe Dark Jak) and feel like seeing some vehicles go ablaze...
The Battle Didn't Count: The only times the boss you killed actually IS killed is if it's a weak sub-boss or the final battle.
The Woman Behind The Curtain: Early on Keira's interactions with Jak take place with her behind a curtain and neither of them realize who they're talking to. This raises the question of how Jak and Daxter didn't realize it was her by her voice. Keira can be forgiven as she's never heard Jak speak and Daxter doesn't say anything. In fact she only realizes its Jak when Daxter finally gets fed up with the way she talks to Jak when she's behind the curtain and starts telling her off after staying quiet in the last few scenes.
Daxter: "Let me handle this, Jak. Listen lady, we beat your stupid course, and we can outrace anybody in this city!"
Keira: "Wait! That voice..."
Daxter: "And there's just two things you need to know. One, we don't want to join your stinking race team, and two... you just lost a date with Orange Lightning. Let's go Jak."
Keira:*Throws the curtain open* "Daxter, it IS you!"
The Man Behind the Man: The Metal Head leader to Praxis, who is extorting Eco from him in exchange for keeping the Metal Heads from invading the seemingly safe Haven City.
This Is a Drill: The MASSIVE Drill Platform, the huge drilling machine in the mines that Jak destroys, as well as the Baron's second combat mecha, which uses two drills to try and remove the Precursor Stone from its statue.
Unwinnable by Mistake: Towards the end of the game, Jak gets sent on a mission to the Under-Port. After completing this challenging task, you will be instructed to find the Mechanic at the Coliseum. If, however, you activated a stadium challenge prior to this (for, say, wanting to collect precursor orbs), when you arrive at the Coliseum, the Mechanic is nowhere to be found, and you will be unable to progress beyond this point in the game's story. The only option is to either restart from the beginning, wasting about eleven hours of work, or send your memory card to Sony so they can fix it for you.
If, however, you have a very large amount of precursor orbs, you can master the race you're stuck in, and look around other areas for orbs you've missed, or perhaps Onin's button-pressing minigame. If you get 200 orbs, you can activate Hero Mode, technically bypassing the bug, and meaning that all of your effort for the last eleven hours was worth it after all. If you're already playing Hero Mode, however... well, you're pretty fucked.
Unnecessarily Large Interior: Mar's Tomb as a whole could probably dwarf all of Haven City—the main room alone is as big, if not bigger than a football field! What on earth did Mar need all that extra space for?!
Unusually Uninteresting Sight: The Krimzon Guard don't notice you until you hit one of them, unless you're taking on certain missions. Also, no one seems to be bothered by the fact that Daxter is a talking rodent who rides on Jak's shoulder.
Urine Trouble: There's a cutscene in which the crocadog pees on Kor's walking staff. Jak and Daxter find this amusing; Kor does not.
Used Future: Haven City features grungy industrial areas, rusty floating vehicles, and badly polluted waters, despite being a futuristic city. The surrounding areas are even worse, thanks to the Metal Heads.
Vampire Refugee: Jak learns to control his Dark powers throughout the game by exchanging large quantities of Metal Head Skull Gems with a Precursor Oracle located in the Water Slums.
Video Game Cruelty Potential: The game allows you to beat up and/or kill the many pedestrians of the city. While it may send a few Krimzon Guards your way, it won't have any effect on the story. This is also possible to do in stadium races by causing other racers to crash—this can even be done with Erol (9:26).
Metal Kor: Don't you recognize him? The boy is you, Jak.
What Could Have Been: As you can see from the Toonami promo for this game, Jak was originally supposed to have the horns he has in Dark Jak mode throughout the entire game. For some reason, this was scrapped from the final game, but there is a glitch where if you walk right near the mirror in Krew's bar, you'll see the horns flicker in and out.
According to one magazine, there was a side mission where Jak would compete with some guys in a Jet-Board competition. This was ultimately scrapped from the final game.
Wire Dilemma: Parodied in a cutscene near the end: Daxter crawls into the Piercer Bomb in order to get the Precursor Stone back and, theoretically, disarm it. He says things like "Should I clip the blue wire?" before just deciding to break a few more things to see if anything comes loose. It works.