Taking place after the events of Big Willy Unleashed, Natalya Ivanova's clone only had a four year life span, and died several years before the game's events, leaving Crypto to lament over her death, while Pox is only reminded and annoyed by the fact that the emergency cloning chamber was used on a human, instead of him. After these events, Crypto 138, having resigned his presidency and gone into an alcoholic binge, has crashed his old saucer into the Space Dust casino's electronic ticker display while drunk, and was killed in the crash. After the crash, Pox has cloned Crypto 139, and they have taken over and re-opened the casino, called the "Space Dust," (A parody of Stardust Resort & Casino) which they use to maintain a steady flow of cash and Furon DNA. They discover that the Molinari Brothers, a mob group, has sent a spy to gather information on them. Crypto infiltrates their casino and destroys the interior, driving out the customers, causing the Molinaris to go to war with him. He defeats the mob, destroys their profits and taking control of Las Paradiso.
Soon he begins hearing a voice instructing him in the paths of enlightenment and how to advance in those paths. As Crypto begins to discover the potential of his powers, strange creatures suddenly appear and attack. Pox identifies them as Nexosporidium Warriors (Nexos), whom are supposedly extinct. Crypto manages to defeat them. In an act of desperation, Pox commands Crypto to destroy all of Paradiso, including the Space Dust, to erase any evidence of their being there. Crypto reluctantly does so, and they flee to Sunnywood.
In Sunnywood, the duo assume C. Curt Calvin, leader of the Lunarian Church of Alientology, to be another DNA harvesting Furon on Earth. To draw Calvin out, Crypto and Pox seek the help of local reporter Veronica Stone. Crypto rescues her after she is kidnapped by the Lunarians, and she tells him of an inside man in the Lunarian cult, known as Deep Navel. Crypto works out an agreement with Deep Navel to meet Calvin, but Deep Naval fails to fulfill his part of the bargain. Pox and Crypto then stage a "big alien arrival" at the Sunnywood Bowl to attract Calvin. Crypto confronts the cult leader and demands he show his true Furon form. Suddenly a Nexosporidium Walker appears and steps on Calvin (this reveals that Calvin is actually a human). After defeating the walker, Crypto is shot in the neck with a dart and faints.
Crypto awakens days later in Shen Long in a monastery ran by a Furon martial arts expert known as The Master. After a confrontation, Crypto agrees to become The Master's new disciple. He reveals to Crypto that one hundred years ago imperial traitors marked Emperor Meningitis, supreme ruler of the Furon Empire, for death. He managed to stop the assassination, but was in turn marked for death. Fleeing to Earth, he crash-landed off the coast of China. He sought revenge, but soon realized eastern philosophies could help him improve his mental abilities, and so immersed himself in the ways of their culture, and in the process lost his desire for revenge. He built an academy, gaining followers to pass his knowledge down to. He took an apprentice named Saxon, who became power hungry, forming a triad called the White Dragon Kung Fu Society to oppose The Master.
The Master instructs Crypto to hold a tournament to draw Saxon out, however Crypto arrives back at the monastery where he witnesses Saxon kill the Master. Enraged, Crypto tracks down and confronts Saxon, who tries to destroy Crypto with a mysterious dragon. Crypto interrogates the villain at gunpoint when Nexos show up but Saxon dies in the confusion, and Crypto escapes destroying the barge. Pox states that the nexos could only have been cloned on Earth, and that only one organization could accomplish such. Pox and Crypto then set off for Belleville, France, home of Francodyne Industries.
In Belleville, Pox and Crypto discover that Francodyne's CEO is Henri Crousteau. Crypto infiltrates Crousteau's mansion to confront him, but Crousteau escapes after stabbing him with a spiny fish. Pox and Crypto escape the mansion and learn Crousteau intends to create a virus to destroy the Furon DNA within the human genome. Crypto sets out to destroy his Nexo manufacturing operation. He causes a riot between the workers and destroys the nexo laboratory. However, Crousteau still manages to create the virus and sends four Nexo walkers to distribute it into the river. Crypto destroys the walkers and faces Crousteau in a final battle at the Belleville tower. Upon defeating Crousteau, Crypto learns that he only wanted to destroy his own race to stop the planet from being polluted, that he was feeding the Nexos synthetic DNA, and that he wasn't responsible for the attack on the Space Dust. The Nexos that did attack were rogue ones responding to a signal from Furon. Crypto then realizes that the one truly responsible for his troubles was Emperor Meningitis himself. He and Pox set off for the Fourth Ring of Furon to confront the emperor.
Upon arriving, Crypto immediately attacks the palace in a blind rage. Enraged, the emperor kicks them out of the city and puts up a large shield. Pox and Crypto manage to deactivate it and re-enter the city. Pox reveals that since he once worked for the emperor his biometrics were still in the system, and would allow them to open the palace door. After doing favors for two Furon workers, Endometriosis and The Librarian, Crypto and Pox download Pox's clone data from the imperial repository, and proceed to clone Pox a new body, becoming Orthopox 14. However, Endometriosis accidentally uses the wrong body mold, and Pox comes out of the machine with a simian appearance. Pox informs Crypto they'll need a distraction, and to start a human riot in the artificial human habitat. As the riot ensues, Crypto confronts Meningitis, defeating him, but the emperor disintegrates from old age before he can be interrogated.
The Master then reappears from the Jade Talisman that Crypto inherited from him, revealing that he was the conspirator who set everything in motion. It was he all along who had been controlling the Nexos, introducing the synthetic DNA, and staging his own death. The Jade Talisman was really a cloning device used so that after Meningitis was defeated he could be smuggled in and become the new emperor. Crypto, shocked by what he has heard, becomes infuriated, and makes a motion to Pox. Pox then uses his strength to slam The Master against a wall, killing him. Crypto picks up a canister of synthetic DNA and tries it, but vomits at the horrible taste. Pox tells Crypto that as long as he cannot stomach the synthetic DNA, their mission wasn't a sham, and there would always be a reason to "destroy all humans". Crypto realizes that Pox is right, and decides to return to Earth. Pox then tells Crypto he isn't returning with him, and takes the throne. As Crypto leaves he states that he will see Pox in the next sequel in ten years. As he dramatically walks out of the palace, the other Furons begin running in, to greet their new Emperor.
- The Master - an old and wise Furon martial arts expert, who has strong mental powers and is well trained in Psychokinesis. He was once a Furon warrior who was friends with Emperor Meningitis, who crash landed on Earth (particularly Shen Long) while on the run from conspiring traitors back home. He longed for revenge, but while on Earth he immersed himself in Eastern philosophies and developed new Psychokinetic abilities, losing his desire for revenge.
- Nexosporidium Warriors (also known as Nexos) - a mysterious race of supposedly extinct cyborgs from the Furon home world.
- Emperor Meningitis - the emperor of the Furon Empire. He always mistakes Crypto's name as Klepto.
- Curt Calvin - the leader of the Lunarian Church of Alientology. He is thought to be another DNA harvesting Furon in disguise, but is revealed to be a regular human.
- Henri Crousteau (a parody of Jacques Cousteau) - a French oceanographer and environmentalist. He discovered The Master's crashed saucer in 1971, and used the technology and synthetic DNA to manufacture his own army of Nexos.
- Saxon (likely inspired by John Saxon from Enter the Dragon or possibly Harold Saxon from Doctor Who who was an alias of the Doctor's enemy known as The Master another named character in the game) - a previous student of The Master who has turned from his discipleship. He wears a yellow jumpsuit made of silk and rides a Nexo Dragon.
- Rolo (likely a parody of Bolo Yeung from Enter the Dragon) - Saxon's right-hand man who is self-obsessed with his pectoral muscles. He is responsible for stealing The Master's Jade Talisman, and for gathering martial arts experts for a tournament, at Crypto's request. After Saxon's death, he rises up to become the leader of the White Dragons. Rolo may look tough, but he's really just a pitiful wimp.
- Jack Trippleson - an actor Crypto uses as a disguise in Sunnywood. He is a parody of Jack Nicholson. Ironically, Crypto hates his voice, even though he sounds very similar.
- Veronica Stone – A female reporter with an obsession of paranormal activity, and the host of a show called "In Quest for..." (a parody of In Search of...). After Crypto tries to lure her out for questioning with the Venus Human Trap, she is captured by the Lunarians, and after which is later rescued and defended by Crypto.
- Molinari Brothers - Mikey is the head of the mob family that Crypto is at war with. He is in charge of the Nero's Palazzo casino, and is the one who declares war on the Space Dust. His brother Vinnie carries a bat with him, smokes cigars and he is overweight.
- Endometriosis - the Furon responsible for making clone body molds on the Fourth Ring of Furon, and the Furon who made a major breakthrough in clone technology. Endometriosis has a Italian accent, and wears a beret.
- Helicobacter - Endometriosis' arch rival and the Furon in charge of the Cloning Industrial Island.
- The Librarian - an old friend of Pox's, this Furon is the proprietor of the Humania Amusement Park, and also the furon in charge of storing highly classified genetic clone data.
- Sammy and Faire (parodies of Sonny & Cher) - two singers Crypto meets in Las Paradiso.
- Travis Skeever, or "Skeeves" - a redneck (though the other rednecks consider him a hillbilly and they strongly believe there's a difference) that lives in the Nevada Desert. He was abducted by Crypto and Pox five years before the events of Path of the Furon. However, his mind wipe implant failed and he kept in contact with a friend in the military, reporting even the slightest sign of alien activity using the world's most powerful citizen band radio. He is paranoid since his abduction and keeps himself locked up in his hillside trailer. After discovering the implant's failure, Crypto and Pox brainwash him to claim that he had made up his alien reports.
- Murray - a human supposedly working for Crypto and Pox at the beginning of the game, but found out to be a mole by Pox. He is the first human killed in Path of the Furon and is used for the Zap-O-Matic, Cortex Scan, and PK tutorials. He either dies or gets knocked out after he gives Crypto information and the angry Furon PK slams him headfirst to the ground.
- Mr. Condo - the owner of the luxury condominium complex on the Fourth Ring of Furon. He is annoyed by the dropping value of his condos due to an asteroid cluster blocking the view, and a group of Nexos who have set up a training ground nearby only seen in the first Odd Job of the Fourth Ring.
Furon technology and weaponry
Weapons such as the Ion Detonator will no longer harm Crypto. Almost all of the previous weapons have been redesigned. The Ion Detonator can now stick to both people and objects, and has a larger blast radius than in previous games. The Anal Probe can now lock onto more than one human. The jet pack has a longer-lasting battery, and controls differently. The Dislocator (introduced in Destroy all Humans! 2) also returns, firing pink gravity defying energy disks that fling people and objects in many different random directions. The player may now engage in "car surfing" via this weapon, and the disks are now pink, instead of purple as they were in Destroy All Humans! 2.
Some of the new weaponry includes the Tornadotron, the Plasma Cannons, the Black Hole Gun, and the Venus Human Trap. Another new weapon is the Superballer, which fires out a supercharged ball that homes in on targets sending them bouncing. With each bounce, the victim takes damage, and with each impact a shock wave is created that affects anything nearby. In a reference to one of the ubiquitous symbols of the 1970s (rainbows) the vapor trail creates a spectral refraction effect akin to a rainbow.
The saucer has been redesigned, as Crypto crashed the original saucer into the Space Dust casino while drunk. His saucer can now fly horizontally and vertically and aim in all directions. Crypto can use the saucer's weapons to scar buildings and terrain. These scars remain until a new mission is started, the player travels to a different location, or in the case of a building, until it's destroyed. The Quantum Deconstructor can now be charged. The saucer can abduct multiple humans, which are processed instantly. When abducted, humans slightly recharge the saucer's shields and also increase DNA.
Controls and Gameplay
Due to streamlined controls, Crypto can shoot humans, use the jetpack, and activate Psychokinesis simultaneously. Crypto can now engage in aerial battles. There are now flying enemies, such as helicopters and Nexo saucers that can attack Crypto in his saucer. The player can travel to different locations "without ever leaving the game world". Buildings collapse and scar differently when attacked with different weapons. The game features a modified alert scheme with police, SWAT, military awareness, and Nexo alert. Electricity surges through power lines when damage is caused to them. The player can now use Mental Lock as an accurate targeting system for circle strafing with a weapon. The player can exit and enter certain buildings freely during some missions, such as the Space Dust. The Master's monastery can be accessed at any time. There is also no fall damage in the game.
Psychokinesis is now mapped to its own trigger for easy access. Using it generates a large blue-purple glow around Crypto's hand. The Temporal Fist ability allows Crypto to stop time, manipulate objects, set up a powerful push, and then resume time. Objects can be given a directional impulse that causes the object to fly with greater force than a normal psychokinetic push once time has been resumed. PK Magnet allows Crypto to magnetize any object in PK, causing several people or other objects to stick and form a ball of humans and debris. Crypto can now use Cortex Scan to prolong the life of his body-snatched victim, similar to the ability of Cortex Scanning humans to refill concentration and keep the Holobob disguise active in the first game.