The X-Factor team and baby Nathan Christopher leave the church after the memorial service for Madelyne Pryor.
Bobby comments that although the Goblin Queen was formidable, they were the only ones to attend her funeral. Hanks reminds him that she never had a real life, being Jean’s clone, and it was fitting that they were the ones to have seen her to her final resting place. Bobby and Warren note that they attended two funerals that week, Madelyne’s and Candy Southern’s. Hank hopes they won’t be required to attend another for a long time.
Lagging behind the others, Jean walks with Scott and baby Nathan. Scott can’t believe that Madelyne would try to sacrifice her own son, even though she was under the evil influence of N’astirh. Jean reminds him that they were all caught in a trap, starting with Mr. Sinister cloning Jean to create Madelyne. Scott hopes that Nathan Christopher will understand when he’s older. Hopefully he can forgive them, replies Jean, as they saved the world but couldn’t save his mother.
Unbeknownst to the team, they are being watched from above by Nanny and the Orphanmaker in Nanny’s ship. They watch Nathan Christopher, as they only need to kill Cyclops to make Nathan an orphan and take him freely. Nanny also has an interest in the babies kidnapped during Inferno that X-Factor will be returning to their families. Orphanmaker says they should take Nathan now, but Nanny wants to wait until they can take all the babies from X-Factor’s custody.
X-Factor’s sentient Ship welcomes them home and notes that its scans have picked up a shadow in the clouds above them. Bobby brushes it off as they greet Artie and Leech. Elaine and John Grey, Jean’s parents, rush over to see Nathan Christopher. Mrs. Grey says that since Madelyne was Jean’s genetic duplicate, Nathan really is their grandchild. She then asks Jean if she knows where her sister Sara and her children, Gailyn and Joey, are. Jean replies that they are still looking for them. She doesn’t have the heart to tell her mother that the robot Nanny kidnapped Gailyn and Joey while she was saving Nathan Christopher. Scott assures Mrs. Grey they’ll find her grandchildren after they return the kidnapped babies to the FBI in Washington.
Artie, Leech and Taki approach Scott and tell him they are ready to go back to school. Scott congratulates them on their help defeating the demons as the X-Terminators and a few minutes later the kids board the plane.
From Nanny’s ship, Orphanmaker asks her if they can take the mutant children. Nanny tells him their primary concern is the babies.
Below, Boom-Boom and Rusty help bring the babies to the plane. Tabitha is happy about not having to go back to school due to the time they have missed and the school’s nervousness over mutant-related incidents. Rusty frets about having to return to naval prison, but Hank assures him they’ll talk to the powers that be in Washington and try to help him.
Scott and Jean say goodbye to Nathan Christopher, who is staying behind with Mr. and Mrs. Grey. Jean worries about leaving Nathan, but Scott reminds her they can’t take him everywhere with them and he’ll be safe with her parents and Ship.
X-Factor’s plane takes off, followed closely by Nanny’s ship. Scott asks Jean if something is wrong, if she’s still worried about leaving Nathan. Jean tells him she’s worried about the babies, that they were used for their mutant power. She feels guilty about abandoning Joey and Gailyn to Nanny, right after she had railed at Madelyne for abandoning Nathan Christopher. Scott comforts her, reminding her Nanny at least cares for children, whereas the demons were going to kill Nathan.
As their plane arrives over Washington, Nanny attaches her ship to them with grappling arms and the plane crunches to a halt. As they prepare to board the plane, Nanny quotes a nursery rhyme while Orphanmaker ponders how they will get into X-Factor’s plane. As if on cue, Cyclops blows a hole through the plane roof and Nanny and Orphanmaker are able to drop in.
Cyclops shoots an optic blast at Nanny, demanding to know where Gailyn and Joey are. Orphanmaker, concerned for Nanny’s safety, opens fire on Cyclops with his gun.
Archangel rushes to Scott’s side and shoves him out of the way, unleashing his paralyzing wing knives at Orphanmaker, but the wing knives merely bounce off his armor. Jean quickly throws a telekinetic shield over the babies to protect them from the ricocheting wing knives.
Meanwhile, Beast hops onto Nanny’s armored head, but is repulsed by her defense shield and is hurled into her ship’s control board. Nanny cries out that he destroyed her ship’s controls and the ship begins to waver in the sky.
Orphanmaker is distracted by Nanny’s cries, allowing Cyclops to tackle him from behind. Scott offers to trade Orphanmaker for Jean’s niece and nephew, but Nanny merely yells at Orphanmaker to use his repulsor field to repel Scott.
Suddenly, Archangel flies by Nanny, using his razor-sharp wings to tear through her armor. She screams, and Warren wonders how a robot can have a scream that human. Nanny’s ship, with X-Factor’s plane attached, ceases to hover and begins to plummet down towards the Washington Monument.
Jean uses her telekinesis to gently set the ship down in the park. The Orphanmaker sees Nanny lying on the ground and runs to her side. Warren explained that it screamed and then the ship lost power. Orphanmaker yells at Warren for calling her an “it”-she’s a real person!
He proceeds to tell them that Nanny used to be a scientist in cyborg technology, and worked for the Right. When she learned the Right had used her technology to create super-soldiers to destroy mutants, she tried to stop them, as she was a mutant herself! The Right captured her and locked in one of her own cyborg designs, planning to enslave her permanently. This nearly drove Nanny insane, but she managed to escape. Orphanmaker explains that Nanny eventually rescued him from Mr. Sinister, who planned to destroy him, as he was too uncontrollable and dangerous. He was at Sinister’s “orphanage”, like Cyclops, but Nanny found him and he became her first “Lost Boy”.
Beast asks where Nanny keeps the other “lost” boys and girls, but Orphanmaker refuses to tell him. Jean, following a hunch, tears apart a wall in Nanny’s ship. Inside she finds Joey, Gailyn and other children hanging suspended from the wall, asleep.
Jean gets them down and awakens them, but is alarmed when the children don’t recognize her. Jean asks where their mother is, but the children respond that they don’t need a mother, that they are Nanny’s orphans. Jean, with tears of fury running down her face, yells at Nanny for using chemical dust to warp the children’s minds and tells her to turn them back or she’ll rip her apart bolt by bolt!
Nanny tells Orphanmaker that their gamble did not pay off and that it is better to run away and live to fight another day. A cloud of smoke forms around them, and they teleport away, leaving their ship and the children behind.
Several hours later, X-Factor releases the babies and the children Nanny had on her ship to the authorities. Mystique, Blob, and Pyro of Freedom Force greet them. Mystique commends X-Factor for rescuing all these children during Inferno and from Nanny. Because of this, and Freedom Force’s recommendation, Rusty Collins has been released into X-Factor’s custody until his naval hearing. Joey and Gailyn will return with Jean, but Blob assures them the other children are on their way to being reunited with their families.
A worried Ship soon sends a transport to pick up the team, along with Gailyn and Joey. Jean worries that Nanny was right about the children being orphans, and something has happened to her sister Sara. Scott doubts it, as several of the children Nanny had have been reunited with their parents. Jean is relieved that Sara is out there somewhere and they’ll eventually find her.
When the transport arrives back on Ship, Beast bounds out to give Rusty the good news about his furlough until his trial. Jean tells Mr. and Mrs. Grey she has a surprise for them, and Joey and Gailyn rush to their grandparents. Although they didn’t recognize Jean or remember their mother, they know their grandparents. Mr. Grey tells Jean that the children will come home with them, where it’s safe and quiet. Jean, saddened by all that’s gone on, agrees with him.