The game is set in the Shadowrun universe, in the 2050s. A time where the blending of technology and human flesh is common; it is around the time the Matrix, a huge computer network, came online, with the ability to jack into its cyberspace directly. It was also a time of magic renewal: a phenomenon known as The Awakening occurred, where magic returned into the world. Sorcery was once again possible, and slowly and seemingly at random humans began to mutate into orks, elves or trolls. This time of upheaval was not without political conflicts: mega corporations began to control the world. But with their magic, native shamans threatened them and the world geography came to a complete change. The Amerindians and Elves reclaimed an area called Salish-Shidhe, close to the free city of Seattle, a major city in the newly formed United Canadian and American States.
Shadowrun's story takes place in these areas, both the wilderness of the Salish-Shidhe and the pollution of Seattle, controlled by mega corporations. Seattle itself is divided in many areas:
- Redmond Barrens: Dark slums only active because of the Shiawase Atomics Nuclear Plant and the Hollywood Correctional Facility, as well as a few other generic shops. The Halloweeners gang resides there.
- Downtown Seattle: The city center, with many bars and corporation buildings. Lone Star, Seattle's police, patrols every hour to ensure order. The Space Needle lies here.
- Penumbra District: A high-class area; only top clubs and corporative buildings can be found in this district. It also houses Lone Star's offices, as well as the Eye-Fivers gang.
- Renraku Arcology: An enclosed city on the power of Renraku Corporation, built inside a pyramid. Many top-class shops can be found here, as well as the massive Renraku offices. Renraku uses their own security team to keep order in their Arcology.
- Puyallup Barrens: Home to the Ork's gang, as well as factories, black market stores, a number of shady bars and hotels.
- Council Island: Neutral lands between the city and the wilderness, and usually peaceful. Orks and humans have an embassy where they live without hatred or discrimination. A bar, stores and a clinic can also be found in the Island. It also has a post where citizens can ask for a visa to enter the Salish-Shidhe.
- Salish-Shidhe Indian Lands / Elven Lands of Sinsearach: Amerindians and elves live in peace with nature in these savage and dangerous lands. Many dangerous creatures can be found here, as well as the occasional hunting party. The Salish-Shidhe and Sinsearach are connected through a complex network of caves that house many paths and secrets. A visa is needed to (legally) travel to the Salish-Shidhe.
- Ellisia's Tomb: The last resting place of the founder of the Sisearach and the "greatest elven hero", it lies deep within the Salish Shide and the Sinsearach, its exact location lost with time. It can't be accessed until the end of the game.
The corporations that exist within this Shadowrun's world are:
- Lone Star Security Services; law enforcement agency in the city of Seattle.
- Fuchi Industrial Electronics, dealing with cyberterminals and Matrix technology.
- Mitsuhama Computer Technologies, dealing with computers and robotics.
- Ares Macrotechnology, dealing with weapons and defense industries.
- Aztechnology, dealing with magic equipment.
- Renraku Computer Systems, dealing with computer technology.
Shadowrun's story begins on January 31, 2058 in Seattle, UCAS. In the wilderness of the newly reclaimed Amerindian lands of the Salish-Shidhe, a small team of shadowrunners is brutally ambushed by unknown forces. The massacre is over quickly, but is captured in video by one of the slain member's cybereyes; the video is recovered and made national news. The last man to die in the video was a shadowrunner known as Michael, Joshua's brother.
Joshua spends his last nuyen and flies to Seattle, vowing to avenge his brother's death. He arrives at Sea-Tac Airport and traces back Michael's last credstick transaction to "Stoker's Coffin Motel", in the Redmond Barrens. Joshua travels there to inquire about his brother, only to be told by the owner that Michael never paid his bill and in fact has some belongings being held. He strikes a deal with Joshua, and by beginning to do small shadowruns for a small-time Mr. Johnson, called Gunderson, he gains enough money to pay his brother's bills.
In Michael's belongings, he finds three holo-pixes: one of a young woman, Tabatha Shale; of an Amerindian, David Owlfeather, and of Seattle General Hospital Dr. Heaversheen. From there, the story divides into three branches that the player can go through in any order, either separately or at once. Each branch gives the answer to three main questions:
- Who killed Michael, and under whose orders,
- What was Michael's last shadowrun,
- Why was Michael killed.
Because of the sandbox style of gameplay and the non-linear story, the entire mystery isn't revealed until the three main branches are totally completed. Once they are, the plot slowly arises:
- Decades before Michael's death, the Salish-Shidhe lands were reclaimed by a number of Amerindians and Elven heroes; amongst them was a man known as Ellisia, who founded an elven Council, the Sinsearach, to protect the wilderness from the city's corruption.
- After Ellisia's death, his body was sealed in a mausoleum with a number of magical artifacts to prevent the misuse of Ellisia's magic power.
- It is then that an ancient free spirit entity called Thon, begins a plot to fully penetrate this world using Ellisia. Free spirits are cursed, as Thon needed to replenish his life force or his form in this world would cease to exist. In order to stay alive, Thon seeks out magical artifacts and in destructive rituals, absorbs their energies. With the power of Ellisia's body and artifacts, Thon could become a physical entity.
- Thon begins to use two Mr. Johnsons, Vigore & Jarl, to carry out his plans for him,
- A mega corporation, Renraku, becomes involved with Thon through Vigore, a corporate support at the time. Renraku begins to work with the free spirit in a top-priority project, "Project THON". The project's leader is Mako Sochou, but he soon is blinded by Thon's promises and betrays Renraku, being replaced by Ito Ogami. Renraku itself plans on manipulating Thon, being the only ones with a map to Ellisia's Tomb.
- By this point, Sinsearach Council member Harlequin sets on a mission to stop Thon from desecrating Ellisia's Tomb and being freed again. To do this, Harlequin asks his apprentice Frosty to hire a Mr. Johnson, Caleb Brightmore, to organize a small team of shadowrunners to go into Ellisia's Tomb and destroy Thon's magic source. Michael is employed in this team.
- Ito Ogami sends a Renraku Strike Team to kill Michael's team; Harlequin is left powerless without his team.
Joshua's mission and investigation eventually leads him to Harlequin himself; but it is not after he completes all stories that the ends meet and he can finally reach Ellisia's tomb, the final stage of the game.
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