Shadowrun

Shadowrun is an action role-playing game for the Sega Genesis, released in 1994 in North America only. It was adapted from the cyberpunk role-playing game Shadowrun by FASA, and developed by BlueSky Software. The game is the second video game adapted from Shadowrun, and has a more open ended style of gameplay than its 1993 precursor, Shadowrun by Beam Software.

Shadowrun's story begins on January 31, 2058 in Seattle, United Canadian and American States. 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 'holopix': one of a young woman, Tabatha Shale; of an Amerindian, David Owlfeather, and of Seattle General Hospital Dr. Heaversheen. There is also a low grade cyberdeck, along with a credstick containing 500 nuyen, which could have been used to pay off Michael's bill (the irony of this is one of the game's many humorous points).

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 is not 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.