The Black Womb Project was a secret government research project based in Alamogordo, New Mexico. Its main purpose was to research the genetics of mutants and studied thousands of mutant children before it was shut down in Mike Carey, Scot Eaton, Mike Deodato and Brandon Peterson's X-Men: Legacy #211-214. In this 2008 storyline, Dr. Nathan Milbury, also known as Mister Sinister, was spearheading the project with Dr. Amanda Mueller, and neither one was worried about the morals of it.
Officially, Amanda Mueller was the head of the project, but Mister Sinister never misses an opportunity to collect genetic data on mutant DNA. Mister Sinister was born Nathaniel Essex in the 1800s and was a masterful geneticist who believed that science should not be shackled by moral implications. He believed that human evolution should have no limits and based all of his work on Charles Darwin’s survival of the fittest concept. After Essex got involved with En Sabah Nur, also known as Apocalypse, he was given mutant DNA to enhance his mind and body, thus becoming Mister Sinister. The Black Womb Project was a convenient and effective way for him to continue his work on collecting and using genetic DNA for his own strength and abilities, and he used the alias Nathan Milbury to join.
Amanda Mueller was no saint herself and was as ruthless a scientist as Mister Sinister. Mueller was born in the 19thcentury with a genetic mutation that allowed her to age slowly. She was married to Daniel Summers at one point, which makes her the ancestor to Cyclops, Havok, and Vulcan. The X-Men name recognition doesn’t stop there because Brian Xavier and Kurt Marko were both on the Black Womb Project team as well. If these names sound familiar, it is because they are the fathers of Charles Xavier and Juggernaut, respectively. As part of the research team, they allowed Mueller and Sinister to perform experiments on their kids. Lastly, Irene Adler was the archivist for the project. She was also known as Destiny and had a romantic relationship with Mystique.
Mueller and Sinister had a good relationship as the two leads of the Black Womb Project, but that all changed when Mueller found out about Sinister’s Cronus Device. This machine was built as a contingency in case Mister Sinister died. The Cronus Device could take a surrogate and wipe their mind and body clean, allowing Sinister to imprint his mind and physical matrix onto it. However, for the machine to work, the surrogate needed Mister Sinister’s DNA attached. With this in mind, Sinister implanted his DNA seeds into Brian Xavier and Kurt Marko, making their descendants viable surrogates. After Mueller discovered this project, her relationship with Sinister became strained because she wanted to use it for herself.
When Mister Sinister died, Mueller used her knowledge of the Cronus Device to try and take his powers by recalibrating the machine. Unbeknownst to her, the machine already started calling a surrogate from the DNA seeds and took control of Charles Xavier. Mueller decided that the only way she could take Sinister’s power was by killing Xavier before the machine imprinted Sinister’s body onto him. Fortunately, Gambit stopped this from happening and destroyed the device, freeing Xavier from its grip.
Currently, Mister Sinister is sort of working with the X-Men. Xavier and Magneto created a mutant island called Krakoa, where they hoped the mutant race could start over and grow. They needed someone with extensive knowledge of mutants and their genetic makeup to help research and chronicle the evolution. Since Mister Sinister had devoted his life to the collection of this type of data, Xavier and Magneto thought he would be the best mutant for the job. Luckily, before his death, he created an island full of his clones. So, Xavier and Magneto went there to enlist his help.
To entice Mister Sinister to take the job, they allowed him access to mutant DNA he had never before collected, including their own. Sinister agreed to the offer and was put in a team made up of other morally ambiguous mutants. The offer wasn’t enough though, and Sinister’s ethically obscured view on the evolution of life got the best of him. He decided to continue harvesting mutant DNA for his own nefarious purposes rather than for the prosperity of mutant-kind.
In the "X of Swords" event, Krakoa was put in a tournament with a rivaling sentient island named Arakko. Sinister used his influence to join the tournament and procure more samples of mutants. He did so with selfish intentions and ended the plight by killing his team so that his machinations stayed unfounded. Whether it’s the 19th or 20th century, whether he’s the original or a clone, Mister Sinister lives up to the name bestowed upon him by his dying wife. To all he meets, he is “utterly and contemptibly sinister.”