In the game's beginning, set ten years after the original, it is learned that, in 1969, the main character from Destroy All Humans!, Cryptosporidium 137, is now deceased for reasons unknown, and his clone, Cryptosporidium 138, made of more complete Furon DNA, is now taking his place and continuing to pose as the United States President. KGB intelligence reveals early on that Crypto 138 is the first and only Furon to have genitalia since the Martian War, which is referred to only as "The Package". It is likely that the KGB is unaware of what "The Package" actually is. Also, Crypto's commander from DAH!, Orthopox 13 (Pox for short) is tagging along and working on restoring his own "package", but he is soon killed when the mothership is shot down by a KGB missile right when he restored it.
Soon after, Crypto's new adventure begins, having to stop the KGB from destroying America and getting revenge for the destruction of the mothership (as well as for ruining the party he was at). But Orthopox, before getting killed, downloaded himself into a HoloPox Unit, and is still Crypto's commander in the form of a hologram. The Soviets, under the control of Agent Oranchov, are planning to destroy Bay City using Revelade, a new health drink promoted by hippie guru Coyote Bongwater. Crypto defeats Bongwater and manages to prevent Revelade from being dispersed, before attacking The Rock, a prison island in the centre of the bay and defeating the KGB.
After saving Bay City from nuclear annihilation at the hands of the Soviets, Crypto discovers that the KGB have fled to Albion and heads there, where he meets Reginald Ponsonby-Smythe, the James Bond-esque head of MI6. While there, Crypto, Ponsonby, and a rogue KGB agent named Natalya Ivanova discover that the KGB have created a type of spore that causes humans to mutate into monsters, and must be destroyed at the source. Eventually Ponsonby betrays Crypto, revealing he is really leader of the English equivalent of Majestic-12 from DAH!, Majestic Command-16. After managing to kill Ponsonby, Crypto learns that the KGB have a base on Takoshima Island (as well as a cryptic warning that Crypto may not be the only alien on Earth...) and heads there in his quest for revenge and the destruction of the spores.
Crypto discovers that the KGB have teamed up with a ninja sect known as the Black Ninjas, who are fiercely opposed to the White Ninjas (who worship Furons). There, Crypto has to rescue a man named Dr. Go! from the Black Ninjas and the KGB who provides a code into the KGB base hidden in the island's volcano. Once there, Crypto and Natalya are addressed by the villain behind all the game's happenings, Soviet Premier Milenkov. Milenkov reveals his men using spores on an intern, who transforms into a giant Godzilla/Gojira-like monster called "Kojira". After defeating Kojira, Crypto heads to Tunguska, home of the KGB.
In the USSR, Crypto discovers that another alien race has crash landed on Earth. They are called the Blisk, and turn out to be the enemies the Furons supposedly destroyed millennia ago. Also known as the Martians, though the locals seem to think they are strange yetis or monsters. Pox realises that the Tunguska strike of 1908 was actually a downed Blisk Warship that was thought to be a meteorite crash-landing into the Tunguskan hillside. After rescuing Natalya from a Blisk Poison Bubble, Crypto meets Milenkov face to face, before the man retreats to his moon base, Solaris, in a Blisk shuttle.
On the moon, Crypto discovers that Project Solaris is actually a Blisk superweapon designed to bombard the Earth with spores and let the Blisk have control of Earth as an irradiated, water-logged planet. Crypto takes on the form of a spokesman (similar to the first game) and convinces the cosmonauts to go to war with the Blisk, after telling them that they are taking away their vodka. Crypto and Natalya battle for their various species to save the Earth, though Milenkov enters after the last battle and shoots Natalya in the back. He then reveals his true form: a massively armored Blisk (apparently, all Soviet leaders before him were also Blisk in human disguises).
After defeating Milenkov, Crypto relaxes in his saucer while Pox appears and tells Crypto that he has detected activity in the cloning pods--he then realizes that Crypto has cloned Natalya. Lying next to him, she's appeared to give in to his lustful advances (Crypto states he made a few adjustments) while they return to Earth.
Arkvoodle, Lord of the Sacred Crotch:
Voiced by: Jim Ward
An ancient Furon god who came to Earth thousands of years ago. Statues dedicated to him are scattered throughout the world and act as landing zones for Crypto's saucer. Crypto has founded several cults around the world in his honor, as Crypto himself has come to embody a Furon prophecy about the second coming of Arkvoodle due to his newly acquired genitalia (leading to the nickname, "Lord of the Sacred Crotch"). Arkvoodle also has a pet: an ancient Furon called the Burrow Beast that can be summoned to eat enemies from below.
Voiced by: Richard Tatum
A hippie that Crypto rescues from the Bay City police, Shama Llama goes on to become the apostle for and manager of Crypto's worldwide Arkvoodle cults. After becoming too cocky and declaring himself the leader of the Arkvoodle cult, Crypto kills him for insubordination. The newspaper that announces his death states that he is likely to be replaced by son of Sleepy Ernst from Destroy All Humans!. He also has an Indian accent.
Voiced by: Richard Horvitz
A Bay City hippie who knows practically everything that goes on there, due to radio messages he picks up with his teeth. Thanks to drugs, he has a hard time recalling anything useful. He's a skilled artist that ends up designing posters for the Arkvoodle cult.
Voiced by: Richard Tatum
A hippie commune leader dedicated to overthrowing "the man" and the creator of Revelade. Initially working with the KGB to accomplish this, he regrets this decision when he finds out they have betrayed him and actually want to destroy America outright. Crypto kills Bongwater, putting him out of his misery.
Agent Ivan Oranchov:
Voiced by: Robin Atkin Downes
The lead KGB agent in America, he betrays Bongwater and leaves him for dead in an attempt to use nuclear bombs to destroy Bay City. He is later killed by Crypto after he is infected with spores and turns into a Blisk mutant.
Voiced by: Yuri Lowenthal
A Takoshimese scientist that knows much about the KGB and Black Ninjas. He is allied with the White Ninjas and Crypto.
Voiced by: Jim Ward
Natalya's former lover who provides information for her, Crypto hates him because of his own feelings for Natalya. Sergei, however, does not share Crypto's hatred; contrarily, he understands Crypto's feelings for Natalya, but looks down on him as though he were a young child. After being infected with Blisk spores, Sergei is never heard from again.
Voiced by: Phil Morris
The janitor (and cook) aboard the mothership, he downloaded himself onto a Holopod, like Pox, to survive. Later found as a Datacore and used as a weapon. He apparently had a large collection of Furon folk music before the attack on the Mothership.
Voiced by: Keith Ferguson
A Military sergeant who has Crypto do a couple of jobs for him, like capturing Clayton Cartwell Jr. (an AWOL hippie who wants to avoid the draft) and kill a rogue military soldier, Private Mendaza who is selling bazooka crates to the KGB. All is well for Fauxhall until a KGB agent tells a disguised Crypto to kill him and retrieve the bazooka crates.
Voiced by: Paul Nakauchi
The Leader of the White Ninjas. He and his group originally wanted to be black but the other ninjas put their order in first when grey was no longer being made. This sparked a war between them. The White Ninja Leader and his men worship Furons and are the "good guys" of the ninjas. He seems to be a little eccentric, judging from the fact that he kidnapped a girl from the super market and was going to sacrifice her, and thinks it's okay because of what Crypto did to Miss Rockwell in the first game.
Voiced by: Steven Jay Blum
The Black Ninja Leader and his men ignited the war between them and the white ninjas by putting their order in first for black clothing when grey was not made anymore. He and his men are in league with the KGB and are the "bad guys" of the ninjas, like how they attack civilians, cops and the Military. The Black Ninja Leader is the person who orders a disguised Crypto to kill Shama Llama.
Leader of the West Yakuza. To differ from the rest of the West Yakuza, Hirotaro wears a peace sign on his suit. He gives a disguised Crypto one mission to lure Kenji Mojo, leader of the East Yakuza into a trap, because Kenji said "His wife was prettier than Yamanosuke's." However, because of a West Yakuza snitch, Kenji Mojo isn't killed. Yet. Hirotaro orders Crypto to kill the snitch, but he still wouldn't feel better. After Crypto kills the snitch, he goes to a KGB agent disguised as one himself to be told to kill both Yamanosuke Hirotaro & Kenji Mojo.
Leader of the East Yakuza. When Kenji Mojo tells Yamanosuke Hirotaro his wife was prettier than Tojo's, Hirotaro, enraged, orders a disguised Crypto to call Kenji to come to a meeting with him as a set up to kill Kenji. But Kenji is one step ahead of his nemesis, because a West Yakuza traitor tells Kenji the entire plan and he escapes death. The West Yakuza traitor however, is killed by Crypto because he's a rat. When Crypto gets a mission from a KGB agent to kill the 2 Yakuza leaders, Kenji Mojo, along with Yamanosuke Hirotaro is killed.
Voiced by: Courtenay Taylor
Prudence is Coyote Bongwater's girlfriend who tries to get everyone to love Revelade because she firmly believes that Revelade will change the nation. She can be killed while the only time she is there after her Revelade meeting.
In one of the Bay City missions the player can communicate with other Furons besides Pox. This can be done by transmitting a telephone call which is picked up by a non-helpful Furon working at Space Traffic Control who Pox insults. The call is then picked up by the Furon Admiral, Cyclosporasis, who denies Pox any assistance. Pox is infuriated by this and the Admiral hangs up.
Zap-O-Matic: Same as in the original, this gun fires bolts of electricity at targets, stunning them. It is now more powerful, but fires in a shorter burst. Largely ineffective against armored vehicles, but lightning can chain between human targets when upgraded. It no longer has the old lightning style firing mechanism.
Anal Probe: Returning from DAH!, the Anal Probe no longer needs to be charged, but now requires ammo. The probe will drill into the target's anus until their head explodes. The probe can also un-infect humans who have been mutated by Blisk spores. This weapon is useless against vehicles and Blisk warriors, but can take out most humans in one hit (assuming they aim for the anus).
Disintegrator Ray: The Disintegrator Ray, as its name suggests fires globs of molten plasma. It is largely unchanged from DAH!, but it can be upgraded differently.
Ion Detonator: It allows Crypto to fire a powerful ion bomb and detonate it at will (regardless, it detonates in 10 seconds). Like the Disintegrator Ray, it is largely unchanged from the original game, except for the upgrades.
Dislocator: Sends a purple gravity defying disc at the target causing them/it to be hurled in random directions. Often the object will fly in the direction of Crypto, forcing him to dodge it. Only a certain number of disks can be flying at one time (this number can be increased with upgrades, and maxes out at 4). The Dislocator, unlike other weapons, regenerates its own ammunition. Each disk ends its run by flying up into the air and dropping the subject. The more disks attached to heavy objects (like tanks, cars) the higher and easier they fly through the air.
Meteor Strike: Allows Crypto to call down a Peterbilt cab sized meteor to destroy the target. It is best used against buildings. When upgraded, it is able to call down multiple meteors and even a small planetoid. This is one of the most powerful weapons in the game (second only to the Quantum Deconstructor) but can, and will, kill Crypto if he is caught in its blast radius.
Gastro: This gun drops Gastro, the mothership's former janitor and cook. He had downloaded himself into a holo-pod during the ship's destruction and obtained a plasma gun that shoots ion shots, which he uses to attack nearby enemies and draw their fire. After upgraded with his "Anti-Everything Launcher," the explosion will cause damage to everything, including friendly characters.
Burrow Beast: Lobs out a lure causing an underground alien worm to chase and devour the target(s) that are near the lure. The lure can also be moved psychokinetically or transmogrified (which yields huge amounts of ammo for other weapons in the game). It is not effective against buildings, bosses or vehicles. This is the "super weapon" that Shama Llama tells Crypto about and is the game's Hidden Weapon made available after finding 30 alien artifacts and completing all 'Arkvoodle Cult' missions. This weapon has also been known to devour teammates in co-op play.
Saucer weapons and abilitiesEdit
Death Ray: A returning weapon that fires a heat ray. The death ray cool down speed is faster than the first one, and it has greater attack power and greater range. The weapon must cool down when used continuously. The saucer starts with this weapon.
Cloak: Makes the ship invisible, but makes you unable to use weapons to save power. Its power drains continuously when used, but recharges over time.
Abducto Beam: Picks up humans and vehicles. Humans can be sucked into the saucer while held in the beam, and used in the gene blender.
Drain: Drains energy from vehicles to replenish the saucer's shields. Vehicles can be destroyed if energy is completely drained from them.
Anti-Gravity Field: Creates a small point of high gravity, which pulls anything close, then explodes, destroying anything pulled in.
Sonic Boom: Launches a sonic blast that is very powerful and can level buildings. Though returning from the first game, the look and sound of the cannon is different, and it is less powerful.
Quantum Deconstructor: The Saucers most powerful weapon. Launches a green blast that can destroy enemies and buildings with ease, and has a huge splash damage area.
Turret: During cooperative play, one player is able to man a four cannon turret armed at the bottom of the saucer. Like the Death Ray, the turret will overheat with extended use and must be cooled down. It fires highly explosive energy blasts that look like disintegrator ray's energy blasts, and they can destroy cars and tanks in one or two shots, but they can destroy buildings but it will take time.
Abilities and DNAEdit
To get new abilities, Crypto must gather Furotech Cells scattered across the world as well as improve his abilities using the Gene Blender. Below is a list of all the abilities:
Body Snatch: Allows Crypto to take over the body of another person (replacing Holobobbing from the first game). Once in a body, Crypto's energy bar will be replaced with that of the current host, which steadily decreases. When it reaches zero, Crypto is expelled and the host is killed. If Crypto expels himself early, the person will still be alive (albeit, with less health), and if they are an enemy character, they may attack. Body snatching becomes required to enter certain areas restricted to certain player types (eg: a player needing to snatch a Secret Agent in order to sneak past other Secret Agents on an assassination mission.) It should also be noted that the way Crypto is expelled out is reminiscent of the chest-burster from the Alien series of movies (albeit in a less violent manner). Free Love: Causes everyone within a certain radius to start partying, forcing people to forget that they saw Crypto for the duration of the power, or for Crypto to body snatch without being detected. In each country, the victims of free love dance differently.
Extract: Extracts the brains of humans.
Mind Flash: This allows Crypto to stun every human in the world for a short duration of time, and resets the Alert Meter. This ability needs DNA (brains) to recharge, which can be collected by using Extract or the Anal Probe.
Follow: Causes civilian characters to follow Crypto.
Protect: Causes armed characters to follow and protect Crypto.
Forget: If someone sees Crypto use bodysnatch, he can make them forget about it. Also, if he has made someone follow or protect him, this will make them become normal again. This will also make person(s) stop dancing when in free love mode.
Psychokinesis: Shortened in the game to PK, it allows Crypto to move people and objects with his mind. Unlike the psychokinesis of the original game, the power does little damage to other characters if used to slam them into the ground or buildings, and it does not require concentration to use. The best way to kill enemies with this power is by throwing them in water. (This ability is famous for its glitches. Defeated enemies can get stuck in the ground or walls if they were PK'ed against them, usually flailing around until they either die, becoming unstuck, or completely stopping all movement.)
Transmogrify: Destroys vehicles or objects by crushing them and converting them into ammo. This also functions as a weapon of sorts, since it can be used to take out tanks or vehicles full of hostile troops.
Cortex Scan: While using body snatch, he can read human minds and Blisk minds. Most of the thoughts will be funny, and when in certain missions, reading minds could help find people and places. Unlike the first game, you can only read minds when in a human disguise (unless extract is not an option at certain points in the game).
Gene Blender: This allows Crypto to abduct humans and mix their DNA, helping him to unlock certain upgrades for Psychokinesis and Body Snatching.(This can also be used to unlock Art Galleries e.t.c)