Throughout early 1999, The Undertaker and his Ministry of Darkness had been feuding with WWF owner Mr. McMahon, trying to gain control of the Federation. To break Vince's spirits, they began targeting his daughter Stephanie. Worried about his daughter, Vince shifted focus from his Corporation stable to Stephanie. With Vince occupied, his son Shane gradually took over the leadership of the Corporation. On April 12, Shane kicked Vince, Pat Patterson, and Gerald Brisco out of the Corporation. His rationale was that there was no room in the Corporation for the old and that Vince no longer had his priorities straight. Shane then slapped his father, saying that the strong, ruthless man he knew was gone.
Heading into WrestleMania XV, Vince McMahon had been feuding with Stone Cold Steve Austin for an entire year. By this point, the Corporation was involved in the feud as well. The Rock, Vince's handpicked champion, lost his WWF Championship to Austin at WrestleMania XV, and also lost a rematch at Backlash. Rock blamed the loss on Shane, who had been guest referee and accidentally hit Rock with the championship belt near the end of the match. The following night on Raw is War, Rock insulted Shane and hit him with the Rock Bottom, and was in turn fired from the Corporation.
At Backlash, the Ministry kidnapped Stephanie. The Undertaker attempted to wed and sacrifice her the following night, but was ruined successfully by Stone Cold Steve Austin after two failed attempts by Ken Shamrock and the Big Show. Members of The Corporation had wanted to help Stephanie, but Shane held them back apparently trying to convince them that it could be a Ministry trap.
On April 27, the pilot episode of SmackDown!, The Undertaker merged his Ministry of Darkness with Shane's Corporation to form the Corporate Ministry. The two groups united in order to fight their common foes Stone Cold Steve Austin, The Rock, and Mr. McMahon. The members of both factions seemingly forgot their past conflicts and worked together as a massive stable.
On the following episode of Raw is War, a new faction formed to oppose the Corporate Ministry. Former Corporation members Ken Shamrock, Big Show, and Test joined together with Mankind to form The Union. The Union members felt that they were being screwed over by the Corporation ever since Shane had taken control of it from his father. Wanting revenge on his son, Vince soon united with the Union as they fought with the Corporate Ministry.
As the Corporate Ministry's first act, Shane ordered a WWF Championship match at Over the Edge between Austin and Undertaker with himself as a special guest referee. However, WWF Commissioner Shawn Michaels countered by adding Vince as another guest referee. That night, an altercation between the feuding McMahons collected Undertaker and Austin, and Shane fast-counted the pin to give the match and the title to Undertaker. That same night, The Rock defeated Triple H via disqualification and The Union defeated The Acolytes, Viscera, and Big Boss Man in an elimination match. A week later, The Acolytes defeated X-Pac and Kane to win the WWF Tag Team Championship.
Meanwhile, The Undertaker's claim that he served a higher power was expanded upon. Eventually, The Undertaker decided to offer Austin to this greater power, who revealed his identity to Austin while dressed in a black robe and a hood that hid his face from the audience. On June 7, the identity of the higher power was revealed as Vince McMahon, and the entire exercise had been a ruse designed to allow the McMahons to get revenge on Austin. After the unveiling, Linda and Stephanie McMahon, who were also victims of the ruse, used their combined 50% share in the WWF to punish Vince. Linda stepped down as CEO of the company, naming Austin as her replacement. Further, she and Stephanie were signing over their shares of the WWF to Austin.
The McMahons challenged Austin to a winner-take-all handicap match at King of the Ring. The match became a ladder match after Big Boss Man lost a match to Austin, allowing Austin to pick the stipulation. To punish him for the loss, Big Boss Man was fired from the Corporate Ministry.
With Steve Austin now feuding with the McMahons, The Undertaker faced a new challenger, The Rock. After Rock beat The Undertaker and Triple H in a handicap match, The Undertaker faced The Rock at King of the Ring for the title. Undertaker won the match, thanks to a run-in by Triple H. That same night, Vince and Shane defeated Austin in a ladder match to win his 50% share of the company and regain full control of the WWF. The following week, The Acolytes lost their tag team titles to the Hardy Boyz. The Big Boss Man rejoined the Corporate Ministry the night after King of the Ring.
After King of the Ring, Austin reinserted himself into a feud with The Undertaker by announcing that, while still CEO, he booked himself a title rematch with Undertaker, with the time and place to be determined by Austin. On the Raw is War after King of the Ring, Austin defeated the Undertaker to regain the WWF Championship.
At Fully Loaded, a First Blood match was signed with two stipulations. If Undertaker regained the title, Austin could never challenge for it again. If Austin was to retain, Vince McMahon would be forced to leave the WWF. Austin won by hitting The Undertaker with a television camera after an assist from X-Pac, thus retaining the title and forcing Vince out of the company. Meanwhile, The Acolytes defeated The Hardy Boyz and their manager Michael Hayes to regain the tag team titles, and Triple H defeated The Rock in a leather strap match to become the number one contender for the WWF Championship. Big Boss Man also won the WWF Hardcore Championship from Al Snow. Two weeks later, the Acolytes would lose the tag team titles to X-Pac and Kane.
By the end of July, The Undertaker's relationship with the McMahons had dissolved and the Corporate Ministry was effectively disbanded by Shane McMahon on August 2, 1999.