Cipher used her mutant ability to remain undetected in the Xavier Institute, hiding from a mysterious threat that to this day remains unrevealed. The powerful telepathic X-Man known as Jean Grey, however, was able to barely detect her presence. Because Cipher was so terrified of whomever was chasing her, Grey and her then-husband Cyclops allowed her to remain at the mansion, receive private training, and help others in the background without making her presence known to anyone else.
Cipher made herself known to fellow student Blindfold, whose near-indecipherable manner of language and visual handicap rendered her helpless against a manipulated Beast, whose humanity was telepathically stripped from him by Cassandra Nova. Cipher helped guide her to safety on many occasions and even attacked Danielle Moonstar when she held Blindfold at gunpoint.
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Cipher then began to focus her efforts on the Young X-Men, a group of teenage mutants who had formed under a Cyclops-impersonated Donald Pierce. She, along with a misguided mutant named Greymalkin, tried to defeat Pierce on their own. Greymalkin, who at first appeared schizophrenic when he was actually speaking to the invisible Cipher, was ultimately involved in his defeat.
Once Donald Pierce was outed, the group reformed under the real Cyclops with the X-Men in San Francisco. Blindfold, who had no real offensive capabilities, was put on the sidelines only to assist the team when needed. Another Young X-Man, Ink, also left the team after he discovered he was not a mutant, but instead received his powers through tattoos he were receiving from a mutant tattoo artist named Leon Nunez.
When the rest of the Young X-Men found themselves outnumbered by a gang of empowered thugs called the Y-Men, who received their powers the same way as Ink, Cipher had no choice but reveal herself to Ink and convince him to help his former team. Initially unwilling to help mutants if he was not one himself, he came around and was able to help save the day.
However, once Ink and Greymalkin began interacting more, the two both began to question each other about the mysterious girl named Cipher. Cipher finally decided to make herself known to the rest of the team and began actively participating in missions with them. However, she is still extremely guarded, revealing only necessary information to others and would get snippy with anyone who presses further. Nonetheless, she quickly became a compassionate member having already known them all long before they ever knew her.
Cipher is next seen with Colossus and Surge trying to stop the riots in San Francisco. While the trio scout the perimeter, the Dark Avengers arrive on the scene. Venom (Mac Gargan) attacks them, citing a fight between Colossus and Rockslide, who participated in the riots. Colossus instructs the two girls to flee as he takes on the dangerous villain.
Cipher is a mutant whose abilities include flight, invisibility, phasing/ghosting, maintaining psychic invisibility (for example Emma Frost cannot detect her with her powers, but Jean Grey could), and emitting a bioelectric charge through people she phases through.
Cipher has also displayed proficient abilities in flying jets, having received advanced training as Cyclops and Jean Grey's pupil.