See also Shadowrun (SNES)/Walkthrough.
The player takes on the role of Jake Armitage, a courier who is shot and nearly killed in the streets of Seattle in the year 2050 by a hit squad. He wakes up in a morgue with significant amnesia as to what he was doing that resulted in his near-death—in fact, he was thought to be literally brain-burnt, which he himself felt as if he was when awakened.
As an action RPG video game, Shadowrun combines both the statistical factor in the tabletop game with real-time gameplay. For example, the player controls Jake, moves him around using the controller, and when attacked, must use guns or magic commands to respond. Some battles within the game require sharp reflexes. This is further complicated by the fact that the Seattle in the game is a rather tough city - practically every screen contains at least one hidden assassin who, from random locations, opens fire on Jake; the player must immediately find the source of the attack and respond or risk getting killed.
At the same time, Jake builds up "karma" from killing enemies - on a steady basis from killing regular enemies, and in large chunks from beating bosses. This karma can then be allocated by the player into different attributes, skills, and magical powers. Physical attributes include basic factors as how many hit points Jake has. Jake also has the ability to learn new skills, such as "negotiation" and "leadership," which allows him to haggle prices and to retain the loyalty of henchmen.
As the title of the game implies, Jake is described as a "shadowrunner," a mercenary character common within the Shadowrun RPG. Moreover, in the game, Jake is able to hire other shadowrunners as henchmen. It is possible for the player to win the game without hiring a single shadowrunner.
In interacting with non-player characters, Shadowrun uses an unusual system. Whenever Jake hears a new and unusual term, this word is highlighted, then added to a sort of database of terms he can use. From that point on, when speaking with NPCs, Jake is able to ask them about this new word; only in this manner can a player progress with the game.
The game also includes an unusual way of entering into cyberspace. After a certain point in the game, Jake, using a cyberdeck, is able to hack into computers to retrieve information, as well as gain more money, which in the game is nuyen (noo-yen). During such scenes, the gameplay becomes two-dimensional while an icon of Jake moves through cyberspace, fights intrusion programs, and retrieves data. As in the original RPG (and cyberpunk literature in general), if the player dies in cyberspace, he dies in real life as well.
Beginning in the morgue the brain-burnt Jake must first get his bearings and find out what put him there and who is helping him or not. Immediately bumping into a witness who saw him before, the player is given the option to follow him, where Jake will obtain a weapon and some body armor. It is possible to obtain a lot of items from the first area, although some are decidedly more difficult than others. Eventually arriving at the Caryards, Jake will meet several others as well as be able to fight in the arena for money where there is a series of boss-type one-on-one battles. It is possible at this point, although difficult, to use the gun picked up from the prior punk witness to actually fight and kill all comers up to a certain level; after that, the gun has no effect because body armour negates the low damage. In order to leave the Caryards, one must either pay the "King" or kill him in battle. It is also a good idea for the player to learn the Negotiation skill as this saves a great deal of money for use in weapons and the like. After this, the player receives relative freedom. The part of town Jake immediately enters has a magic item shop, a gun shop, a bar, and a street doc. It is revealed that Jake was carrying a program in his "head computer" that was able to destroy artificial intelligence. Shortly after he got a copy of this program, a corporation trying to construct an extremely powerful AI, aided by a mysterious figure known as "Drake," destroyed both the company that created the program (Matrix Systems) as well as the computer programmer who created it (Raitsov). As Jake has the last-known copy, Drake sends hit men to assassinate him. On the verge of death, Jake is saved by a Shadowrunner named Kitsune. As the game progresses, Jake meets Kitsune, who is apparently attracted to Jake. Unlike other shadowrunners, Kitsune will never leave Jake once hired. Unbeknownst to him, Jake is really a shaman (a possible player class in the original RPG). With Dog as his shamanistic totem, Jake is able to learn and cast magic, as well as gain insight into his situation. The mysterious Drake is in reality a dragon with a secret lair located in a volcano. He must be defeated before Jake can attack the final enemy, Aneki Corporation, which is behind the entire plot.
- Jake's last name, "Armitage," appears to be a homage to the character of the same name in William Ford Gibson's novel Neuromancer, an early cyberpunk novel. Naming a character 'Armitage' seems to be a cyberpunk trope.
- In the Beta 1 version of the game, the people at the morgue are referred to as the "chop shop guys". A later revision of the game replaced this phrase with "morgue guys", as well as making several other minor changes that slightly toned down the game.
- It is possible, as in the original pen and paper game, to hire runners. This reflects the D&D style of group playing, but because the game is a one-player game, the runners follow you closely, and shoot on sight. The max amount hired depends on Jake's Charisma level, and if he has the Leadership skill, he can retain the runner for variable, longer amounts of time. If they die in your hire, they will respawn back at where they were previously (e.g., at the bar) to be hired again; thus, it is a good idea to keep track of the health levels of the party. Depending on the strength and skill value of the character hired, the player can give the character weapons from one's own arsenal, allowing them to shoot for more damage. This also applies to body armor.
- One hired character actually betrays Jake at a certain part of the game, adding depth to the story: if in the player's party at a certain mission point, he will begin to attack Jake. Because the character must be hired first, this makes the betrayal "optional".
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