Mannifestum Rising is the 12th episode of Season 4 and the 52nd episode overall.
When Lee's rescue mission becomes bigger than he ever dreamed of, he soon realizes where all the school's orders are coming from. Now it's up to Lee and his friends to save the day meanwhile Cam and Brandy try to figure a way how to escape out the tunnels and get the key back.
The episode opens inside Maxwell Finnwich's laboratory inside Coral Grove where Finnwich is playing the organ attempting to decipher the page of The Book he took, which evidently is sheet music. Finnwich comments that Alexander always made him work a little harder for everything, reminiscing about the mistake they made over a century ago and commenting that the page he took maybe the key to preventing the end of the world.
His musings are cut short when Cassandra McAdams comes in demanding the long awaited answers Finnwich promised her, starting with what he saw inside The Pyramid, why the Ping family is so important, and what exactly is His Eminence. Deciding to ignore Cassandra's requests once she leaves Finnwich uses the song he's been deciphering to awaken Lynch Webber in order to have him fetch Lee Ping for him.
Meanwhile Holger Holgaart is attempting to entertain his cellmates Lee, Tina Kwee, Biffy Goldstein and Jenny Jerkins. Whereas Biffy is more concerned with finding a way out Lee encourages him to wait until dinner time, when the guard brings Tina her Dinner the five of them will rush it and take the keys from them, prompting Holger to make up another "ghost robot arm" story to entertain them.
The Bell ending school for the day rings prompting Camillio to inform everyone that school is over. One of the Wurst clones however informs the student body that no one is leaving until the Pyramid is in one piece again, reinforcing his claim by revealing a quarantine around the school from a rather nasty diseased lice outbreak. At Coral Grove, Kimmie is doing her best to try and enjoy the "vacation" out on a patio.
Kimmie points out to her mother that normal family's go to beach or ski resorts when they go on vacation whereas they're at a top secret Military base. Cassandra disregards what her daughter says to her and goes back inside Cassandra has a meeting with his Eminence and reveals that she has already captured his ally The Serpent and has been spying on him during his trip to Toronto, where he met with the Ping family and will release the older Ping brother if he tells her the whole story.
Cassandra believes it has something to do with the Ping family, why else would he arrange to have Lee un-expelled. The humanoid creature states that Cassandra should be careful what she asks for, once she knows there's no going back. His Eminence explains that there were originally five members of the group that opened the Pyramid the first time around during the last eclipse.
They are Alexander Nigma A Nigma High's first Principal, Elizabeth Mann Cassandra's grandmother, Dr. R. Wurst whom invented the cloning technology, Maxwell Finnwich the inventive genius of the group and Ping. Meanwhile Holger finishes his four hour long story, prompting Biffy to order him into complete silence. Tina admits to Lee that being with him has made the worst case scenario a little better.
Canning the small talk the group gets into position to incapacitate the guard serving them, only to learn that it is a reawakened Lynch. They do not believe he's working for Finnwich again and instead uses him as a distraction while they escape. Back to Cassandra His Eminence explains that working together the members of the group redirected the energy beam into the pyramid while Alexander unlocked it.
Alexander only realized his error once one of the pods inside opened to release a roughly humanoid creature, His Eminence, and attempted to seal him inside the pyramid. Back at the school the student body devises a plan to keep the teachers busy using a brain teaser contest buying Brandy and Camillio the opening they need to escape and save them. Successfully implementing the first part of plan the pair run into Barrage on their way out and he convinces them to free him.
Back to the story even with the help of The Red Tazelwurm His Eminence escaped anyway leaving Alexander Nigma trapped inside the Pyramid in his place. His Eminence introduces himself to Nigma's students as "the best friend they'll ever have" and marks each of them right down to their DNA, giving each of them and their descendants special marks that forever link them to the Pyramid.
Now in order to complete his plan his Eminence needs each of the marks reunited, meaning Finnwich, the Wurst clones, Cassandra and at least one of the Ping Brothers. Meanwhile Lee's group nearly succeeds with their escape attempt when they sneak aboard the submarine set for A Nigma. Lynch however remotely reprograms the submarine to take them back to Coral Grove and informs Lee that his true mother, the not clone one, is being held prisoner at Coral Grove.
An animation error, however brief, occurred near the episode, to be precise when Barrage asked Camillio and Brandy "What's January doing with September," Barrage's eye-patch appeared to be on his left eye instead of his right.