Beyond Good & EvilEdit
The Lighthouse AttackEdit
The game begins at the lighthouse. Jade is doing yoga with one of the orphans when the DomZ attack. Jade tells the orphans to get into the house while she activates the force field. Suddenly, Jade is informed that her account is empty and the power company shuts off the force field - worse yet, a group of DomZ Sarcophagus have cut off the orphans and taken them hostage.
After saving the orphans, Jade encouters the first boss fight in the form of a Domz Spirit Eater. Pey'j arrives and gives Jade her Dai-jo staff, which she uses to defeat the Spirit Eater. The Alpha Sections arrive late, once again. After the Alpha Sections and the news crew leaves, Jade collapses from the fight. She recovers, but is visibly saddened by the fact that they have no units to pay for power.
Jade's holographic EI Secundo arrives and states that the Science Center wants to catalog all the species on the planet, and needs pictures to complete the catalog, and will pay "mucho credits" for them. After taking pictures of a few animals around the orphanage, Jade is able to get power back online, and she is informed of a job for her from the mysterious "Mr. De Castellac " via Mdisk. He refuses to give details over an unsecured channel, but informs Jade that he can tell her what he wants her to do in person on Black Isle .
Jade and Pey'j set out to meet Mr. De Castellac on Black Isle in their hovercraft. However, the hovercraft breaks down midway, stranding the two out in the middle of the ocean. A tow ship from the Mammago Garage arrives and tows them to the Garage. There, Jade purchases a new engine for the hovercraft using the pearl she took from the dead Spirit Eater.
After leaving the Garage, Hillys is under attack by the Domz again, this time led by a DomZ Sea Serpent. Jade and Pey'j are able to kill the serpent before they resume course for Black Isle. There, Mr. De Castellac's manservent informs Jade that they received a reliable tip that a couple of male and female DomZ creatures are hiding out in the center of the Isle, and if allowed to mate their offspring would overwhelm the surrounding area.
In order for the ministry to take action they would need proof, thus where Jade comes in. Her assignment is to go into the creatures' lair, take a photo of them, and send it to Mr. De Castellac. Only after taking the photo does Jade realize that instead of taking a photo of two miniscule creatures, her assignment was to kill a single DomZ Monster known as a Pterolimax .
After Killing the Pterolimax, Mr. De Castellac's manservent reveals that Mr. De Castellac never existed. He states that his real name is Hahn, an agent of the IRIS Network , a so-called terrorist organization that is actually a resistance group against the Alpha Sections. Hahn states that the Alpha Sections are working with the DomZ instead of fighting them and have been behind the recent mass kidnappings.
The Nutripils FactoryEdit
Hahn Tells Jade to meet him and the Iris Network in the city at the Akuda Bar . There he informs her of the DomZ and Alpha Sections three-part sapient species trafficking operation. First, the kidnapped people are brought to the Nutripils Factory , where they are tortured into submission. Next, they're shipped to the slaughterhouses where they're crated and shipped to the DomZ/Alpha Sections base on the Hillys moon Selene.
Jade's first official assignment as part of the IRIS Network is to infiltrate the Nutripills factory and take photographic evidence of the tortured victims, the Alpha Sections involvement, and finally rescue their agent, Double H , who went missing while investigating the factory. Jade is also informed that she'll need a codename to sign her papers with, and she chooses Shauni. After upgrading the hovercraft with a targeting cannon, the area is besieged by another DomZ attack, led by a second Sea Serpent. This time, Jade and Pey'j are ready and easily defeat it.
Next, they destroy the Alpha Section defenses around the factory, and sneak in. Once inside, Pey'j realizes that a DomZ monster is guarding the area and identifys it as a Reaper , which has destroyed an elevator, Pey'j believes he can squeeze one last go out of it, but needs new parts. After getting separated from Pey'j, Jade discovers that Double H has been hooked into a Domz torture machine. By photographing it, Jade manages to get a warrant for all Alpha Sections codes in the Nutripils factory courtesy of the Governer of Hillys . Using one such code, she gets a Gyrodisk launcher and frees Double H with it.
Unfortunately, Double H falls into the sewers, and he and Jade are separated in the process. After reuniting with Pey'j, they're attacked by the Reaper, a long extinct prehistoric monster reanimated by, and under the control of, a DomZ Spirit Eater. Using the Gyrodisk launcher Jade is able to defeat the monster, and with Pey'j's assistance, gets a fuse to fix the elevator.
With the elevator repaired, they're able to travel deeper into the factory. Pey'j suddenly remembers that they received a mission disk the other day and gives it to Jade.
After being given the Mdisk, Jade goes to scout ahead alone. She sneaks into the x-ray verification room and gets a photo of Alpha Sections overseeing the kidnapped people being loaded onto unmarked ships to the slaughterhouses. While she gets the photo, Pey'j is captured by Alpha Sections. Jade is able to sneak into the security room where she finds security footage of Pey'j's capture, along with his jetboots.
Eventually, Jade sneaks into the factory control room. There she finds the finest proof of the Alpha Sections working with the DomZ, a single guard and head of security working the controls of the factory who is not wearing his helmet and thus is revealed to have DomZ spores implanted into his body, mutated to the point where he is no longer human.
Jade photographs the guard and sends the image to the IRIS Network. After a short amount of time, she finally finds Pey'j, though she is not able to save him before he is loaded into a ship and sent to the slaughterhouses. A Spirit Eater arrives to monitor the area, and the guard from before states that everything is on schedule. However, the Spirit Eater spots Jade and, to both get rid of her and punish the guard for his incompetence, the Spirit Eater rips out his spores, killing the guard and fusing them with some machinary to create the boss for the level. Double H arrives and, together with Jade, defeats the DomZ Machine. However, they soon discover a bigger problem - the DomZ infected Double H with spores while he was in captivity. Double H is able to use the equipment in his suit to buy some time, but they have to get him to the IRIS Headquarters. Once in IRIS, Double H is injected with the antidote, saving his life.
In the meantime, Hahn gives Jade her next mission: infiltraiting the slaughterhouses where Pey'j is currently being held to find more evidence of the smuggling operation, and the DomZ alliance with the Alpha Sections. Thanks to Jade's report from the Factory, the Hillyans have spontaneously shown their support in the form of a rich supply of pearls.
Double H informs Jade that the only way into the Alpha Sections slaughterhouses is through a secret entrance in one of the races run throughout the otherwise abandoned district. With another upgrade to the hovercraft they're able to enter the races, and eventually find the secret entrance in the third racetrack. While inside the slaughterhouses, Jade finds evidence of the kidnapped victims being tortured and packaged, as well as cloning chambers containing DomZ Sarcophagi.
On their way back to the city, the area is bombarded by a third DomZ Sea Serpent attack, but Jade and Double H are able to defeat it easily. At the IRIS den, Jade meets the Governer of Hillys, who gives her a keycard to the Alpha Sections' most secure areas. After that, the team suddenly receives a call from the IRIS leader, "Wild Boar", who Jade recognizes as Pey'j.
Pey'j tells everyone that he is being held on the moon, and tells Jade to read the Mdisk and find the ship. Based on the information given to them by Pey'j, they form a plan: find Pey'j's ship, go to the Alpha Sections/DomZ moon base and broadcast Jade's reports from their long range transmitter to the people of Hillys, thus prompting the Hillyans to rise up and join IRIS in a final assault.
Jade is devastated to learn that while she was investegating the Alpha Sections in the slaughterhouses, the Alpha Sections had attacked the lighthouse and kidnapped the orphans. After defeating the remaining Alpha Sections on the island, Jade becomes distraught by the loss of the orphans. Inspired by Double H, Jade soldiers on. Reading the Mdisk, Jade discovers that the bottom of Pey'j's jetboots each contain a code that, when entered into two separate panels, unveils a secret hangar where a partially damaged ship known as the Beluga is being kept.
The Moon BaseEdit
After repairing the Beluga and giving it spacefaring capabilities, Jade and Double H go to the Selene base on the moon. There, Jade finds Pey'j's freshly drained corpse and decided to finish what she started, to avenge him. She scouts on, coming across the leader of the Alpha Sections, General Kehck , and the High Priest of the DomZ having a conversation.
After taking the photograph, Jade attempts to return to the ship. On her way there she is informed by IRIS that Pey'j is alive and just messaged them. She goes to meet her uncle and, when she asks how he's alive, he explains that Jade's always had a potent power brewing deep within her and she accidentally used it to bring him back to life.
The three of them sneak into the transmitter room, where Secundo hacks the systems and uploads Jade's photos onto the very screens the Alpha Sections have been using to broadcast their propaganda. With this, the Hillyans rise against the Alpha Sections and prepare to launch an assault on the Selene base.
In a last ditch effort to kill Jade and her team, General Kehck activates the transmitter's auto destruct, and when that fails, he fights them in a massive military ship with a tractor beam. Eventually they sink the ship, but the tractor beam is still active. They succeed in deactivating the tractor beam and Jade herself confirms that General Kehck is dead.
The Revolution, The Finale Battle, The EndEdit
The Hillyans and IRIS network arrive just in time to help fight off the combined remaining forces of the Alpha Sections and the DomZ. In the meantime Jade, Double H, and Pey'j all go to confront the DomZ High Priest. The Priest tells everyone present that Pey'j has been lying to Jade for years - her body is just the latest in a long line of vessels used to keep the power of the DomZ away from them, and she is the reason why the DomZ have been attacking Hillys and killing its people to stay alive. He tell them that Jade has inadvertently lured the people of Hillys into a trap of the Priest's crafting. Following a long fight against the Priest where Jade has to fight DomZ clones of her two companions, she finally destroys the DomZ and, using her power, she revives the people of Hillys.
In post-credit scene, Pey'j is looking over a rebuilt light house, when suddenly he begins to convulse and a DomZ spore erupts from his hand.