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Dr. Nefarious returns to take control of the Great Clock, a "marvel of science and sorcery" that regulates time throughout the universe, and is located in the exact center of the universe... give or take fifty feet. As in Secret Agent Clank, the duo spends most of the game separated, trying to reunite and stop Nefarious, while they both learn the truth about their respective pasts.
- Anti-Villain: General Azimuth, who risks destroying the universe in an attempt to bring back the Lombaxes using the Clock.
- Apocalypse How: The initially harmless-seeming Fongoids caused a Class X-3 in the backstory, destroying 83 star systems. Dr. Nefarious' plan to misuse the Great Clock for his own benefit would instead have caused a Class X-4. General Azimuth very nearly DID cause one.
- Art Shift: Flash Backs and photographs are typically drawn rather than CG rendered
- Arguably, the entire game's art style is one. Compared to ToD, it looks a lot more cell-shaded and cartoony.
- Ascended Extra: The Groovitrons and Mr Zurkon, both just 'combat devices' in Tools, become fully fledged, upgradable weapons in this game. Given that both were major Ensemble Darkhorses, this comes as no surprise.
- Back from the Dead: Via the "six minute rule" as mentioned by The Plumber, Clank is able to briefly use the clock to prevent Azimuth from killing Ratchet.
- Bag of Sharing: While wandering the Great Clock, Clank can destroy boxes and repair things to earn bolts. That Ratchet can use to buy things.
- Bread, Eggs, Milk, Squick: Fred's hobbies are listed as moonlight strolls along the beach, reading, and mauling unsuspecting enemies with brutal efficiency.
- Bring My Brown Pants: "So much for clean underwear."
- Captain Space, Defender of Earth!: Captain Qwark.
- Continuity Nod: This has a lot, possibly due to its likelihood of being the last game in the series. (Except it wasn't.)
- Cool Old Guy: Orvus. Guy saved the universe and created Clank. Loves puns. Also perhaps the most quotable character in the entire series.
- Cosmic Keystone: The Great Clock.
- Crosshair Aware
- Cutscene Incompetence: Near the end, Ratchet and Clank and Qwark are surrounded by guards and Dr. Nefarious and naturally surrender because, well, it's a cutscene. Never mind that there are only like eight guards, and they later fight Nefarious with basically the exact same level of preparation.
- Damn You, Muscle Memory!: R1 was used to zoom in for the past games' Sniper Rifles. In this game, it's the fire button. Be prepared to waste a lot of ammo getting used to the Plasma Striker.
- Developer's Room: The Insomniac Moon, unlocked by collecting all 40 Zoni and defeating Lord Vorselon for the final time. Filled with Dummied Out content.
- Disney Villain Death: Cassiopeia. Though Lawrence has another theory on why she disappeared...
Lawrence: Perhaps she thought about marrying you and decided to make a run for it.
- Don't Explain the Joke: Orvus is prone to this.
Orvus: Did you see what I did there?
- Dumb Muscle: The Agorians. Though they're actually Genre Savvy enough to recognise this and hire another race (see My Brain Is Big below) to do the thinking for them.
- Dying Moment of Funny: Nefarious. Even if he isn't really dead.
- Eccentric Mentor: Orvus.
- Eldritch Abomination: The Rift Ripper 5000 summons one of these. It's called Fred...
- Empty Room Until the Trap: Lampshaded. After going through two of these in the Valkyrie Citadel, Ratchet is not surprised by the third.
Cassiopeia: So, you...
- Eternal Engine: The Great Clock.
- Face Heel Turn: Azimuth.
- Failure Knight: General Azimuth is this until he goes a bit crazy and tries to reverse his failure.
- Fantastic Rank System: Alister Azimuth is a "Four Bolt Magistrate".
- Flip-Flop of God: Angela Cross apparently IS a Lombax now, reversing the writers' decision from earlier in the series.
- Fluffy the Terrible: The monster summoned by the Rift Inducer 5000 is named "Fred".
- Also, Snowball, Qwark's Agorian War Grok.
- Fluffy Tamer: Qwark somehow tames a War Grok.
- Foreshadowing: Vorselon's message to Ratchet: "Only one lombax need perish tonight. If you'd be willing to take his place..."
- Frickin' Laser Beams: An unlockable upgrade for the Constructo Pistol.
- Funny Background Event: In the Agorian Battleplex - while Qwark is trying to woo the audience, in the background Ratchet is being mauled by the War Grok.
- Gainax Ending: Parodied. According to a radio broadcast, the season finale of Lance and Janice was one of these. Doctor Nefarious is not happy.
- Game Within a Game: "My Blaster Runs Hot - The Game". It's a twin-stick shooter that has Qwark facing down hordes of robots.
- Hey, It's That Voice!: So Mario is Clank's creator?
- I Just Shot Marvin in the Face: To quote Lawrence: "Might I suggest engaging the safety, so as not to kill any more troops?" Qwark also majorly fails gun safety when he gestures to his "intelligence" by pointing a gun to his head.
- Ironic Echo: When first asked why he didn't leave with the Lombaxes, Azimuth wistfully answers: "Sometimes the universe has a cruel sense of humour". At the end of the game, Orvus concludes his final message to Clank by saying: "The universe has a wonderful sense of humour. The trick is learning how to take a joke."
- Arguably, Ratchet falling at the Great Clock could be considered an echo of the same thing happening on Planet Reepor in Tools of Destruction, OR the aforementioned "mid-air rescue" of Clank at the Valkyries' base.
- Just Between You and Me: Hilariously played with in the trailer:
Ratchet: What is it this time Nefarious?
- Killed Off for Real: This game features an impressive deathcount of important characters: Clank's father Orvus, Alister Azimuth, Lord Vorselon, Cassiopeia, Carina and Libra, Pollyx, and even Ratchet.
- Lies, Damned Lies, and Statistics:
Qwark: This Lombax is young. He does not understand that being a hero is 45% strength, 60% bravery, and 10% raw intelligence.
- Lying Creator: Dr. Nefarious used to be in the Killed Off for Real entry, even had Word of God backing it up. But that was until the first preview pages of the Canon sequel comic came out... and now he's a playable character in the next game, too.
- Macross Missile Massacre: The RYNO V.
- Make Wrong What Once Went Right: Dr. Nefarious' ultimate goal.
- Since this would mean allowing every evil plan ever foiled by the heroes to succeed, from Chairman Drek onward, logically, General Azimuth's plan would have caused this too, since it would have prevented Ratchet from ever meeting Clank.
- Memento MacGuffin: Azimuth's pocket watch becomes one after his Heroic Sacrifice. The hoverboots Azimuth gives Ratchet were originally Kaden's.
- More Dakka: The 'Rapid Fire' mod for the Constructo Pistol. Shoots so quickly even tapping the fire button for a split second will fire off 2-3 shots.
- Made even more ridiculous by the RYNO V, which (in V1) has 1500 ammo and goes through it in around one minute. It also plays the 1812 Overture whenever fired.
- My Brain Is Big: Terachnoids. Loading screen trivia implies that they actually house multiple brains in their massive skulls, as the smartest was born with seven and a half.
- My God, What Have I Done?: Alister Azimuth gets one of these moments after you defeat him, since he's about to get the entire universe destroyed.
- My Greatest Failure: A big plot point in Tools of Destruction was that Tachyon was able to defeat the Lombaxes and conquer the galaxy due to having improved Lombax technology. Crack in Time reveals that Azimuth was the one who gave Tachyon access to the tech. (Ironically, he did so because he believed that Tachyon's improvements would help defend the galaxy.) This mistake weighs on Azimuth so much it drives him a bit insane, which comes to a head in the climax of Crack.
- Mysterious Waif: Clank, more or less. Not a very standard one, but his backstory certainly fits.
- The Problem with Licensed Games: My Blaster Runs Hot is a rare In-universe example.
- Proud Warrior Race: Agorians.
- Put on a Bus: While Talwyn doesn't appear in the game, she does get the occasional mention (For example Ratchet mentions her before crash-landing on Quantos, and she requests a song for Ratchet on Pirate Radio), suggesting that she simply didn't come with him on this particular mission rather than that she dropped off the radar entirely.
- Recurring Boss: Lord Vorselon.
- Redemption Equals Death: Alister Azimuth. Kind of crossed-over with Heroic Sacrifice.
- Set Right What Once Went Wrong: Ratchet and Azimuth's motivation. Later subverted when it turns out it wouldn't really work and Ratchet and Clank must stop Azimuth.
- Shout-Out: Two of the trophies are "It Belongs in a Museum" and "88MPH"
- Smoke Out: Unfortunately, Quark didn't realize the smoke bomb doesn't actually cause Offscreen Teleportation
- Strong Family Resemblance: Azimuth figures out that Ratchet's a real Lombax instead of a holo-guised assassin due to his striking resemblance to his father, Kaden.
- Tempting Fate: Discussed.
Captain Qwark: "The key to surviving situations like this is to refrain from phrases like 'it's too quiet in here' and 'everything's gonna be alright'."
- Too Many Halves: In one of his many boasts, Qwark explains to Ratchet that "being a hero is 45% strength, 60% bravery and 10% raw intelligence". Ratchet doesn't fail to lampshade that something doesn't add up.
- 2-D Space: Played straight to a ridiculous degree when there are force fields in a narrow ring around a planet that you can't get by without disabling.
- More generally the space sections play like this - in comparison to the free-flying in Going Commando and the on-rails sections in Tools of Destruction, Size Matters and Secret Agent Clank, you can only fly on a flat, 2D plane.
- Verbal Tic: All Fongoid males have one. The loading screen trivia mentions that scientists have no idea why it's the case, but also that the leading theory of time travel as the cause was dismissed as "both laughable and impossible" by the scientist who came up with it.
- Villainous Breakdown: Azimuth begins to break down towards the end, attacking (and killing!) Ratchet to meet his goals. His ranting during the final boss battle is also increasingly unhinged; it takes a My God, What Have I Done? moment to bring him down to normal.
- Vocal Dissonance: Libra, one of the three leaders of the Amazon Brigade, sounds suspiciously like Dr. Girlfriend.
- The Walls Are Closing In: Happens at the beginning of the last mission, but Qwark can brace the walls forever, and all you have to do is just blow up some Mooks in the enclosed space before the trap is released.
- We Have Reserves: Dr. Nefarious's response to accidentally killing his minion with an "unloaded" gun is to simply press a Big Red Button to call in the next (completely terrified) minion.
- Well-Intentioned Extremist: General Azimuth after his Face Heel Turn.
- What Happened to the Mouse?: The game fails to resolve several plotlines that Tools of Destruction left hanging. The upcoming comic series may resolve them yet, though.
- It is never revealed what happened to Talwyn's father, Max Apogee, and in fact, Talwyn doesn't appear in the game at all.
- Actually if you listen in on the radio you can catch a report that seems to imply that Max teamed up with Angela from the second game (now apparently confirmed to be Lombax), and docked on Kerchu where they used the Dimensionator to flee to wherever the Lombaxes were.
- At the end of Tools of Destruction, Tachyon yells at Ratchet that he is the only one who knows Ratchet's true purpose in Polaris and his true name. This is brought up in the final cutscene where Clank confirms that he detected no lie in Tachyon's voice. Despite this, this ends up never being referenced again, and Azimuth's account makes it sound like Ratchet being left behind was just a mistake.