Headmistress of the X-Men
Emma Frost and her new love Scott Summers assumed headmasters of the school and X-Men. Most of the X-Men were very bitter and reluctant of their relationship, due to the fact Scott immediately went with Emma minutes after Jean's death. They were also suspicious of Emma's behavior and past and questioned if she was truly loyal to the X-Men.
When Cyclops and Emma Frost started a new team of X-Men in hopes to "astonish" the public (as this team would be their 'public relations' team), Emma recruited Kitty Pryde, the girl whom Emma attempted to kidnap back in her Hellfire Club days. Kitty was disgusted that Emma had joined the X-Men and became the headmistress, so she said she would keep her eyes on Emma.
Rachel Summers, Scott and Jean's daughter from an alternate time line, especially had problems with Emma's relationship with her father. During a mission to investigate the new lineup of the Hellfire Club, Rachel accused Emma of secretly working with the Hellfire Club, which led both to a telepathic battle among emotions, skill, and power. Both telepaths exchanged snarky comments as well as rather hurtful words. Emma remained the victorious telepath in this "battle," however, the moment was bittersweet as Emma claimed she was no longer enemies with Rachel and offered Rachel a chance to refine her telepathic skills. The offer was accepted and both women have had much more peaceful exchanges than in previous times.
House of M & Decimation
When the Scarlet Witch was having problems with her powers, the X-Men and New Avengers were called to a meeting to discuss the fate of Scarlet Witch. Keeping the Scarlet Witch alive would be a danger to all of Earth and some team members wanted her dead. However, other team members of the meeting had a history and/or personal relationship with the Scarlet Witch and wanted her life spared. They believed if they slowly and methodically talked to Scarlet Witch, then perhaps she would be able to control her powers. But before the members of the meeting could take action, Wanda altered all of reality which was known as the House of M. In this reality, Emma lived in Hartford, Connecticut, with her husband Scott Summers. She was a children's counselor and counseled Franklin Richards, a boy whose parents died in a space accident. However, the Summers couple was quickly informed by Wolverine that Scarlet Witch had altered reality. Immediately, through some telepathic revelations through Layla Miller, Emma Frost soon realized her happy life was just an altered reality.
Emma Frost played a crucial role in House of M by helping Layla Miller telepathically inform people of the lies of their lives caused by Scarlet Witch. Finally when the X-Men and Avengers were able to find the Magnus family, including Scarlet Witch, they discovered it wasn't the suspected Magneto who manipulated Scarlet Witch but her own brother Pietro. Magneto turned into a fit of rage and killed his son Pietro, which devastated Wanda. Through Wanda's overwhelming emotions and stress of past events, she uttered the words, "No more mutants." Emma's telepathy, along with Doctor Strange's magic, blocked out Wanda's depowerization effects from the mutants who were there at battle - which is an explanation to why some mutants retained their powers during M-Day.
Through those final words, the entire mutant population was decimated to only 198 mutants. Emma Frost and Scott Summers, the leaders of the X-Men, realized the last of the mutant population needed to be protected in much more aggressive ways. Emma took initiative and ordered all depowered students and faculty staff away from the X-Men's grounds. This action caused much controversy and stress, however, Emma made her word final. Unfortunately, the night the depowered students were loaded onto a bus and away from the X-Men's grounds, an anti-mutant preacher named William Stryker ordered a missile directly at the bus. This killed all of the students on the bus. Once again, Emma Frost felt responsible for the deaths of the children she tried to protect. However, this would not stop Emma from trying to protect her students yet again. Because the mutant population was practically endangered and religious zealots known as the Purifiers were out to kill mutants, Emma and Cyclops ordered the children to practice for battles and prepare for the worst.
Phoenix Endsong & Warsong
Shi'ar, the alien race whose people were killed due to the Dark Phoenix, discovered the Phoenix Force was weak because its "pieces" were missing. The Shi'ar ordered the Phoenix Force to die, however, the force called onto Jean Grey, its host, and resurrected her. With Jean's return, this caused insecurities amongst Emma, who was afraid Scott would leave her for Jean. Scott, however, reassured he wanted Emma and that he would not return to Jean. When the X-Men were battling the Phoenix inside Jean Grey, the Phoenix was confused and thought it needed love - so she looked for Scott. However, this "love" turned into a lust for power and attempted to consume Scott's energy blasts for power. But this ploy by the Phoenix Force was not working - Emma offered herself as the Phoenix Force in order for the force to get what it really wanted (which was Scott. Theoretically, the only way to get to Scott would be through Emma, since Scott loved Emma). However, Emma had immediate problems while "hosting" the Phoenix Force because she did not have enough power (she merely provided a shell for the Phoenix Force). In the knick of time, Jean returned from her absence and ripped the Phoenix Force from Emma. Jean began to lose control of the Phoenix Force, until Scott realized what Jean really needed was her friends to help her survive. Emma gathered a telepathic hologram of everyone who loved Jean and showed it to her - Jean was now emotionally complete and ready to serve the White Hot Room as White Phoenix of the Crown.
The Phoenix returned, yet again, to bond to Celeste, one of the Stepford Cuckoos, and to burn away what didn't work. Emma Frost and the X-Men had to follow the Cuckoos to The World, a place where super powered beings were modified and created as weapons. It was revealed Emma's ova was stolen by John Sublime in order to create hundreds of identical Stepford Cuckoos. These identical clones were harvested some time after the death of her Hellions, when she fell into a coma. The thousands of Cuckoos started to refer to Emma as their “mother,” which Emma later accepted. While Celeste struggled with the Phoenix Force, it was revealed that the Phoenix came to destroy the hundreds of clones. The Phoenix succeeded and then split into the hearts of the three Stepford Cuckoos, which resulted in the consequence of them having no emotions. Emma Frost contemplated on the fact that hundreds of her “daughters” died in the hands of the Phoenix Force; she then promised if the Phoenix ever returned, it would have to deal with her.
When the Civil War began and super powered beings had to register their personal information to the government, Tony Stark (Iron Man) contacted Emma Frost and asked which side the X-Men would choose. Emma stated that they would not side with Iron Man and rather be neutral, fearing that taking either side would put the mutant population in even more danger. Emma then stated if Iron Man and his friends left the X-Men alone, then they should have no fear in the X-Men joining with Captain America. Tony peacefully left and respected Emma's opinion. However, a few weeks later, Ms. Marvel visited the institute and tried to convince the X-Men to join the SHRA. Emma harshly criticized Ms. Marvel, stating that the Avengers were never there for the Genoshan genocide, and, again, stated that the mutants were in too much danger to be involved.
Throughout Astonishing X-Men, Emma spoke to shady mysterious figures which hinted a possible betrayal of the X-Men. It was revealed that these mysterious figures were a new incarnation of the Hellfire Club, consisting of Sebastian Shaw (Black King), Cassandra Nova, Negasonic Teenage Warhead, a mysterious cloaked figure called Perfection, and Emma Frost herself!
Because Cassandra Nova has desperately tried to destroy the X-Men in the past, she created a backup plan and forced Emma's secondary mutation through a machine - this way, Emma would be used by Cassandra Nova in order to infiltrate the X-Men, had Nova's second attack gone bad (which it did). Nova implanted subtle thoughts into Emma's head that told Emma she should have been dead - that Emma survived the death of the Hellions, she survived the Genoshan genocide, and that she was and is still evil. Through Emma's emotionally weakened state, Nova manipulated Emma into attacking the X-Men, one by one. Emma's love for Scott was challenged during this time. She took Scott into his own "Black Bug Room", a place where one's worst fears would be faced and challenged. Emma revealed the reason why Scott could not control his optic blasts was not because of a brain injury, but because he placed his own mental blocks himself, in order to not control his powers. Emma claimed Scott was "free", and left him in an unconscious state.
It was revealed the reason why Nova needed Emma to "betray" the X-Men was simply because Nova needed her consciousness called "Stuff" to gain back full power. Perfection was revealed to be Emma's former evil self, the White Queen of the Hellfire Club. Cyclops, however, was able to gain his consciousness back and stop "Perfection" from merging “Stuff” into the mind of Cassandra Nova. He shot the telepathic projections of the newly created Hellfire Club and revealed to the team that it was only Emma telepathically creating the projections. Kitty was left horrified and traumatized over facing her worst fears and attempted to shoot Emma with a gun, however, Cyclops was able to stop her and explain what happened. Cassandra Nova's plan was thwarted at the knick of time when everyone present was teleported into space by S.W.O.R.D.
The X-Men were transported to Breakworld to stop a bullet from hitting the earth. During this time, Scott admitted he truly loved Emma, regardless of what she had done in the past. Surprisingly, Emma was shocked by what he said and cried because such an "ordinary, extraordinary man" was "in love...with her."
With many delays and interruptions, the X-Men were finally able to rendezvous as a team and put an end to the Breakworld mission at the cost of Kitty Pryde. Kitty Pryde decided to take a look inside the "bullet" to see if she could turn it off [at the time, the X-Men had no knowledge the "missile" was actually a rather large bullet]. Because Kitty was previously having trouble phasing through the Breakworld's metal, she was trapped inside the flying bullet, which was headed towards planet Earth.
Throughout the remainder of the bullet's trip to Earth, Emma Frost telepathically communicated with Kitty and informed her of the plan of rescuing her. However, Kitty insisted she stayed inside the bullet because she had a plan. Unfortunately, the entire superhero community back at Earth was unable to find a solution to stop the bullet from hitting Earth; however, Kitty Pryde played a heroic moment and phased the entire bullet through Earth. It is unknown where Kitty and bullet are now.
Finally, the X-Men landed on Earth to start a new journey. Piotr, Kitty's former love, asked Scott if he was able to get in contact with Kitty through the Fantastic Four or Steven Strange - Scott said no and claimed it shouldn't have been Kitty to disappear. Emma Frost swiftly turned towards the wall and cried with her gloved hands covering her face.
Scott and Emma finally had another chance to be alone together - Scott requested Emma to turn back on his mental breaks restraining his power. "It was a beautiful gift," he claimed, however, the strain was very hard on him. With ease, Emma turned on his powers. Together, they pronounced they loved each other.
Endangered Species and Messiah CompleX
Because mutants were classified as "endangered," the death of an unidentified mutant shocked and surprised the entire mutant community. Cyclops realized he needed to take initiative and no longer be passive with the X-Men dealings. With Emma at his side, she agreed.
William Stryker, religious zealot and leader of the terrorist group called the Purifiers, gathered a large number of other human zealots to kill every mutant on the planet. They even concocted a lab created creature called Predator X, which was a mutant hunting creature able to detect mutants within its range. While the Purifiers were causing havoc on the streets, a group called the Marauders, which was gathered by Mr. Sinister and company, to attack when necessary.
This was an extremely rare appearance as no mutants had been born since M-Day. The X-Men landed in Alaska to find the baby gone and a large massacre around the town the baby was born in. The Purifiers and Marauders had already been at the scene and had already been informed that the baby was born. With all three groups wanting the baby, alive, the search for the baby began only to find Cable, Cyclops' son, with the baby.
Finally when all three groups had their last battles, the X-Men ended victorious. In a telepathic duel, Emma Frost was able to knock Exodus unconscious along with the help of Dust, who generated a cloud of dust around Exodus to interrupt his normal breath flow.
At the end of Messiah CompleX, Cable left with the baby girl and headed for a future in which he would prevent from happening. Following the end of Messiah CompleX, Cyclops initiated major changes within the X-Men: the X-Men were no longer a school. In fact, all the students residing at the mansion were evicted and sent somewhere else. Hellion, who was put into a coma due to Lady Deathstrike's attack during Messiah CompleX, finally woke up and found Emma waiting by his hospital bed. Emma coldly remarked there were no more X-Men and no more school. Hellion bitterly left the school - his whereabouts are unknown.
Emma and Scott went on vacation to Savage Land. Emma claimed she was having the time of her life and wanted her moments with Scott to never end. Scott promised things would change for the X-Men as he no longer wanted a future with dead mutants and dead comrades, as what the past was before. They were both interrupted from their vacation as Angel was having odd problems in San Francisco, California. It turned out Lady Mastermind, who was thought dead in Messiah CompleX, was alive, well, and projecting mental illusions throughout the city that made people believe they were all hippies back in the 60s. Emma Frost was able to stop Lady Mastermind's mental projections and bring the city back to its normal state. The mayor of San Francisco enthusiastically thanked the X-Men for saving the city and even offered the X-Men a place to stay. Because the X-Men's mansion back in Westchester, New York, was destroyed due to past events and the government was not happy with the X-Men's residence there, the X-Men decided to take a new path and move to San Francisco, California.