Although characters from Deus Ex are present, they are in no way connected with the plot of Deus Ex.
Unlike Deus Ex, Invisible War is not a CRPG, but a First-Person Adventure. The Hero/Heroine of the Adventure is Alex D., a test subject removed from Area 51 merely weeks before the collapse. The Player starts as being transferred out of Chicago during a massively-destructive Terrorist Attack by the Knights Templar. They must proceed to worldwide locations from Seattle to Antartica to learn about the conspiracy of the two factions the WTO and the Order.
At the end of the game, the player must choose who will rule the world by obeying their orders.
Although it is a decent game, it is shunned for it's inaccurate physics engine and frowned upon by Deus Ex.