The Ministry of Darkness oficially began when the Undertaker came back in January, 1999, after being defeated by "Stone Cold" Steve Austin in a buried alive match. The Undertaker recruited the first members of the Ministry of Darkness: Faarooq and Bradshaw, making them the Acolytes and he made them paint dark symbols on their chests.
The Undertaker had the Acolytes abduct Dennis Knight, and he was transformed into Mideon. At the Royal Rumble of 1999, the Ministry recruited Viscera. The Undertaker then introduced the next recruitments; The Brood: Edge, Christian and Gangrel.
The Undertaker then announced his intentions of taking control of the WWE from Vince McMahon. The Ministry then began to stalk the McMahon family, in paticular, Stephanie.
The Undertaker gave Shane an envelope, demanding Shane to give it to his father. Vince did not react well to the Ministry's actions towards Shane, or the contents of the envelope: pictures of Stephanie. Vince made the Undertaker participate in an inferno match against Kane.
During the match, Paul Bearer presented Vince with a black gift box containing a teddy bear(presumably Stephanie's). The Undertaker won the match when Kane's foot caught fire. The Undertaker then took the teddy bear from vince and lit it on fire, bringing Vince to his knees, then he left Vince lying, crying on the ramp staring at the bear.
Big Bossman then got involved, and the Ministry sacrificed him. The Undertaker and Bossman fought in a Hell in the Cell match at Wrestlemania XV. When the Undertaker won, the Brood descended from the ceiling and helped the Undertaker hang Bossman from the cell, before ascending back up to the ceiling.
The Ministry then abducted Stephanie, but Ken Shamrock found her in the boiler room when he forced Christian to tell him where she was. Christian was severely punished. He was about to be sacrificed when Edge and Gangrel saved him from the Undertaker. The Brood then left the Ministry.
At Backlash, the Undertaker said that the tragedy would begin that night, and Vince had left Stephanie in their car with security guards outside the car, while he went to watch the main event. During the post-match celebrations of "Stone Cold" Steve Austin, the Ministry minus the Undertaker went to the parking lot where Stephanie was in the car. The security guards told the "driver" to go. Little did they know that the driver was the Undertaker. Stephanie did scream.
On RAW, the Ministry had stephanie dressed in a black gown for an Unholy Wedding with the Undertaker. "Stone Cold" Steve Austin saved Stephanie from becoming the Undertaker's unholy bride right at the last minute.
Shane turned the corporation against Vince before he announced that he was behind the Undertaker abducting Stephanie. This began the Corporate-Ministry Era, where Shane's Corporation joined the Undertaker's Ministry.
For a while now, the Undertaker had been claiming that he answers to a "Higher Power". On RAW, the Corporate-Ministry had "Stone Cold" Steve Austin in the ring, and the Undertaker presented the "Higher Power". It was Vince all along. It was all just a plot for vince to get at "Stone Cold" Steve Austin, proving that vince would do anything to get at him, even using his own daughter in that way.
The Corporate-Ministry Era ended after Fully Loaded in July when Austin won the "End of an Era" first blood match, when X-Pac came out and kicked the Undertaker in the head, giving Austin the chance to get a camera to bust him open with, which set up the Undertaker/Big Show vs Kane/X-Pac feud.