A video trailer created using the game itself was shown during Square Enix's press briefing at the giant games show.
The cyberpunk-themed game once again features augmented human Adam Jensen who this time takes on a role as a cop hunting terrorists.
Square Enix said the game would be released for PC, PlayStation 4 and Xbox One in early 2016.
Mary Demarle, lead writer for Mankind Divided, said it was set in 2029 - two years after the events in the previous game Deus Ex: Human Revolution.
She said the game started with Adam Jensen being inserted into an anti-terror task force as a covert agent seeking evidence that the group is being used by a powerful cabal for its own ends.
As in other Deus Ex games, said Ms Demarle, the choices that players make when investigating or completing missions will influence how the story plays out.
In Mankind Divided these "choices and consequences" had been pushed further so the ending of the game would change completely depending on what players did, she said.
The Square Enix press event saw the firm show footage and trailers for many different games including Rise of the Tomb Raider, Final Fantasy XIV: Heavensward, Star Ocean, Hitman and Just Cause 3. Hitman and Just Cause 3 will both be released in December this year.
The Hitman game, in which players once again take on the role of bald super-assassin Agent 47, has been revamped and it is now set in a large open world. Gamers will be able to explore the environment and take out targets in many different ways.
It gave a glimpse of the realism it has managed to instil in lead characters such as Lara Croft which can now be depicted in high fidelity down to individual skin pores, eyelashes and threads in clothes.
In one of the strangest moments of the show, game designer Yoko Taro delivered a speech about work on an new version of cult game Nier while wearing a grinning mask that resembled one of the characters in the original game.
It also announced mobile versions of the Tomb Raider and Kingdom Hearts games and said it was setting up an entirely new studio in Japan to work on an as yet unnamed role-playing game that has the working title of Project Setsuna.
The first footage from the upcoming Deus Ex: Mankind Divided video game has been unveiled at E3.