McMahon then began an on-screen relationship with wrestler Test, which led to a rivalry between him and her older brother Shane. After Test defeated Shane at SummerSlam in a "Love Her Or Leave Her Match", Stephanie and Test went on to team together in a match on September 20, 1999, with the couple defeating Jeff Jarrett and Debra. The couple were eventually engaged, but during the in-ring ceremony, Triple H showed a video which revealed that he had drugged McMahon and taken her to Las Vegas, Nevada where they were married in a drive-through ceremony. McMahon seemed to abhor Triple H at first, but eventually revealed that she had sided with him and that the wedding was real—a revenge plot against her father for the aforementioned kidnappings, thus turning her into a villain.
In 2000, with Vince McMahon absent as a result of injuries inflicted upon him by Triple H at the Armageddon event in 1999, Triple H and Stephanie became the on-screen owners of the WWF, a period known as the "McMahon-Helmsley Era" and dominated by the McMahon-Helmsley Faction. Triple H held the WWF Championship and Stephanie held the WWF Women's Championship after defeating champion Jacqueline with the help of Tori and D-Generation X on the March 28 edition of SmackDown! On the June 6 edition of SmackDown, Stephanie successfully defended her title against Lita and on the 16 edition of SmackDown. Stephanie reconciled with her father and brother at WrestleMania 2000 when they helped Triple H defend his title against The Rock, leaving Linda McMahon as the only fan-favorite in the McMahon family.
In late 2000, a love triangle storyline began featuring Stephanie, Triple H and Kurt Angle. The storyline continued at Unforgiven when Triple H defeated Angle with a Pedigree following a low blow from Stephanie, proving her loyalty to him. Stephanie later became Angle's manager and was in his corner when he defeated The Rock for the WWF Championship at No Mercy. The alliance was short lived, however, as after The Rock performed his Rock Bottom maneuver on Stephanie at No Mercy, Triple H attacked Angle, considering it his fault that Stephanie was hurt due to her managing Angle at the time. On the August 21, 2001 episode of Raw, Stephanie lost the WWF's Women's Championship to Lita despite the interfrences from Angle and Triple H after the special referee performed The Rock Bottom on McMahon.
The internal disputes between the McMahons led to Linda McMahon being in a comatose and wheel-chair bound state due to the stress of being asked for a divorce by Vince, who took the opportunity to have a public affair with Trish Stratus. Stephanie briefly feuded with Stratus, defeating her at No Way Out. Over the next few weeks, Vince made it clear that he favored Stephanie over Stratus, allowing Stephanie to bully and verbally abuse Stratus. At WrestleMania X-Seven, Shane McMahon defeated Vince in a street fight. During the match, Stratus slapped Vince and chased Stephanie from ringside, apparently upset with Vince's constant misogynistic treatment of her.
In 2001, she became the leader of the Alliance. Her team "the Alliance" consisting of her brother Shane, Booker T., Rob Van Dam, Kurt Angle and Steve Austin was defeated by "Team WWF" consisting of The Undertaker, Kane, Big Show, Chris Jericho & The Rock at the Survivor Series in a five-on-five, Winner Takes All elimination match. The night after The Alliance was defeated, Shane and Stephanie were banished from WWF television. McMahon returned in January 2002 when Triple H made a comeback as a fan-favorite, but the good couple began having problems, as McMahon began acting like a nagging and clingy wife. As part of the storyline, the couple "divorced" after McMahon claimed to be pregnant in order to trick Triple H into renewing their marital vows. Triple H later discovered that she was lying through a phone call from Linda McMahon and left her at the altar during the renewal ceremony. As a result, after Triple H won the Royal Rumble, McMahon appointed herself special guest referee in a match between Kurt Angle and Triple H at No Way Out with Triple H's WrestleMania WWF Undisputed Champion shot on the line. Though Angle won thanks to McMahon's biased officiating, Triple H defeated him the next night to regain his title shot. McMahon then aligned herself with former enemy, Chris Jericho. Despite interference by McMahon, Jericho lost to Triple H at WrestleMania X8 on March 17. On the March 25 episode of Raw, Jericho and McMahon lost to Triple H in a Triples Threat match for the Undisputed Championship, with the stipulation that, if McMahon was pinned, she would be forced to leave the WWF; In the match, Triple H pinned McMahon.
On July 18, 2002, McMahon returned to the WWF (renamed WWE) as the General Manager of SmackDown!. In contrast to her McMahon-Helmsley era villain character, Stephanie became a fan favorite, as she began to favor fan favorite wrestlers at that time. She feuded with Raw General Manager Eric Bischoff throughout 2002, though the enemies inexplicably shared a kiss at a Halloween party in which McMahon was dressed as a witch and Bischoff was disguised as her father underneath a mask.
Meanwhile, Vince McMahon began to resent Stephanie's attempts to stop him from pursuing an affair with Sable. The feud culminated in the first ever "Father–Daughter 'I Quit' match" at No Mercy. McMahon was accompanied by her mother, the CEO of WWE Linda McMahon, and Sable accompanied Vince McMahon in their match. Stephanie lost when Linda, at ringside threw in a towel on her behalf because Vince would not release a choke he had on her with a lead pipe. As a result of losing the match, Stephanie disappeared from WWE television for two years.
Stephanie returned as a villain once again in October 2005, she, along with her father and, in a surprise twist, her mother fired Raw announcer Jim Ross. A visibly pregnant McMahon also returned on the March 6, 2006 episode of Raw, approaching Shawn Michaels backstage and claiming to have abdominal pains. When Michaels left to get her some water, McMahon pulled out an unmarked substance out of her brassiere and poured it into his bottle of water. This substance caused him to become groggy during his match against Shane later in the night, which he lost as a result. McMahon also appeared at the WWE Hall of Fame induction ceremony on April 1, 2006 and in a backstage vignette with her immediate family at WrestleMania 22.
McMahon returned during a backstage segment in April 2007 at WrestleMania 23, visiting her father before his "Battle of the Billionaires" match. After her father returned to Raw after faking his own death, Stephanie publicly revealed that her father had an illegitimate child, who was among the WWE roster On the taped edition of Raw that aired September 3, 2007, Stephanie, along with her mother Linda and her brother Shane, made several appearances to confront Mr. McMahon about the child, who was later revealed to be Hornswoggle, turning into a fan favorite. On Raw's 15 Year Anniversary episode, she appeared along with Shane in a segment—also involving her father Vince and Hornswoggle—which ended with her kissing her real life husband Triple H, to humiliate her father on Raw.
After the scripted severe injuries sustained by Vince on the June 23 3-hour edition of Raw, Shane appeared requesting for the Raw Superstars to stand together during what was a 'turbulent time'. Shane's plea was ignored, and subsequently, for the next two weeks, Stephanie and Shane urged the superstars to show solidarity. The following week, Shane announced Mike Adamle as their choice to be the new Raw General Manager.
After Adamle stepped down as General Manager, Stephanie soon became in charge of the brand and (reignited her feud) and had altercations with Chris Jericho in the following weeks, which involved her firing him (although he was later reinstated). After her father Vince returned, the family began a feud with Randy Orton, who began the storyline by punting Vince in the head. After a few weeks of feuding, Orton and his alliance, The Legacy, punted Shane in the head and performed an RKO on Stephanie. Following the attack, he was chased out of the ring by Triple H, who is her real-life husband. The rivalry between Orton and The Legacy against Triple H and the McMahons continued at WrestleMania XXV, where Triple H defended the WWE Championship against Orton. The following month, Orton won the championship at Backlash. After Backlash Stephanie left Raw and took a hiatus from WWE television.
Stephanie made an appearance as a guest speaker at the WrestleMania XXVII Press Conference. Several months later, she appeared in a backstage segment at SummerSlam to wish CM Punk luck in his match. Upon offering to shake his hand, Punk declined with the insult, "I would, but... I know where that hand's been." The following night on Raw, Stephanie appeared backstage with CM Punk and with a sadistic glare threatened, "...in the end, people always get what they deserve."
On July 23, 2012, Stephanie made an appearance on the 1000th episode of Monday Night Raw where she confronted and then slapped Paul Heyman to convince him to accept a match between Brock Lesnar and Triple H at SummerSlam. On April 6, 2013, Stephanie inducted Trish Stratus into the WWE Hall of Fame.
On the June 3 Raw, McMahon made an appearance to reveal her decision not to allow Triple H to compete that night. On the June 17 Raw, McMahon confronted new Divas Champion AJ Lee. On the July 8 Raw, McMahon fired Vickie Guerrero from the position of Raw Managing Supervisor when the WWE Universe voted "Failed" during Guerrero's Job evaluation. She turned heel on 19 August 2013 after supporting actions of her husband, at SummerSlam the previous night, and stood beside him. Later in the night Stephanie stood beside Triple H and her father as they celebrated Randy Orton's WWE Championship Coronation, during which Daniel Bryan was attacked by The Shield and subsequently by Randy Orton. Stephanie was at ringside when Triple H lost to Daniel Bryan at WrestleMania XXX.