After learning his trade working as a programmer on games such as Thief: the Dark Project, Chey co-founded Irrational Games with Ken Levine and Robert Fermier.
At Irrational, Jonathan Chey went on to produce, design and program games such as System Shock 2, Freedom Force and BioShock. In 2005, Irrational Games was acquired by Take 2 Interactive.
In 2009, Jonathan Chey left Take 2 to work on new business ventures.