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Irrational Games was founded by former Looking Glass developers in 1997. For some time after opening they struggled with the trials of managing a business, something they had little experience with, and the task of getting a project underway. In a somewhat ironic move, they eventually settled on a partnership with Looking Glass to develop a System Shock-like game using the 'Dark' engine, being written for Thief. Irrational would design the game and do the bulk of the work, whilst Looking Glass would create the a majority of the art assets.
Initially the team went into pre-production on the assumption they would not be able to use the System Shock license. Origin, publisher of the original, had been taken over by EA, and since System Shock had not been a huge commercial hit, persuading EA to publish the game would not be easy. Somehow though, it happened, and they set about creating a sequel which complemented the seminal original, within the constraints of a very short and strict development cycle, staffing problems and the fact that they were piggybacking on an unfinished engine and the resources of another team who were readying their own game (Thief) for release.
System Shock 2 was released in August 1999, less than a year after Half-Life had blown the doors off the first-person shooter genre with its cut-scene-less storytelling and impressive scripted sequences. The Shock 2 team had managed to incorporate similar sequences, though decided once again not to have any living NPCs in the play area whatsoever to avoid killing the immersion with the poorly realised representations which were all that the Dark engine could deliver. You can't blame them; in the opening sequence, the player's character is visible briefly. His face is made up of about two polygons, with a distorted, blurry texture stretched across. This sufficed for hoards of bionic mutants and mutilated chimpanzees, but not narrative which again enlisted the use of retrieved diaries.
System Shock 2 is still by far the deepest game in this sector in terms of character creation. At the beginning of the game the player chooses one of three specialisations and specifies which skills to focus on during their military career before the game's story even begins. The levels are equipped with a myriad of upgrade stations where abilities can be chosen and upgraded, and stats enhanced. Armour can be changed, weapons must be modified and maintained, and there's even a mechanic for researching the remains of enemies for stat boosts. Although a massive step forward from that of System Shock, the game's interface was still rather bloated and required the player to switch between two 'modes' to allow the mouse to be used to navigate it all whilst still be able to interact with elements in the world. Unlike other games which employ systems like this, time would not stand still while the player fiddles with his inventory and hacked security systems, and so opportune moments had to be taken.
Like the original, System Shock received a huge amount of acclaim from the press and has an extremely loyal fan-base to this day. However, sales were not as good as was hoped and shockingly; at the time of writing System Shock 2 has not been in print for many years unlike most other PC games of its calibre which thrive from the budget release market.
As mentioned, Looking Glass were developing the first two chapters of the Thief series at this time. Although the Thief games are strictly speaking stealth-based games, many of the pioneers were on board and they sit firmly lodged in the roots. Unfortunately, the company was better at making innovative games than it was at managing money, and Looking Glass Studios went out of business in 2000.
With Thief 2 released and Looking Glass bust, former employees went their separate ways. Few enough ways for us to continue our story, however...