Story's replacement will be entertainment-based panel show The Project.
Mediaworks has confirmed The Project is replacing Story in the new year, and they expect it to usher in a "reinvention of weeknights", combining current affairs and entertainment in each half-hour episode.
" The Project is news delivered differently," said Hal Crawford, MediaWorks' Chief News Officer.
"At its core will be strong, compelling storytelling. We'll be looking for new ways to explore issues that resonate with New Zealanders, bringing a fresh or unique perspective."
It remains unknown who will be involved after comedian Guy Williams - who recently announced his departure from The Edge - dismissed the idea it might be him, calling the notion "a comical nightmare".
That said, Mediaworks says Paul Henry will make guest appearances on the show and panellists will include Newshub journalists and presenters, comedians, sport, political and other personalities.
The news follows reports from earlier this week, when on Monday, the Herald broke the story that Henry would step down from his breakfast show role.
MediaWorks bosses later confirmed that Story would not return next year.
Mediaworks has now confirmed Story's host Duncan Garner will take over the morning slot but with a whole new show.
The brand new show is called The AM Show and will run 6-9am on weekdays, continuing with Paul Henry's cross-platform approach across TV3 and RadioLIVE.
Garner said: "Paul is a brilliant broadcaster who has changed the game in the mornings - I'm looking forward to building on that. Our new show will be warm, seriously smart, irreverent and funny. I can't wait to rip into it."
It is unclear what's next for his co-host Heather du Plessis-Allan.
Other announcements from the launch also confirmed the Herald's earlier reports that Dominic Bowden will replace Mike Puru as host of The Bachelor NZ when it returns for its third season next year.
Mediaworks also confirmed the return of many of its shows, including local series The Block, 7 Days, Jono and Ben, Family Feud, Westside, Grand Designs NZ and Lost and Found.
The Project and The AM Show are due to begin in early 2017.