I love those types of stories. Recently did something like that with an old player of mine.
His original character concept from way back in first edition was a Decker. The character always wanted to be a mage and was fascinated by magic and all things arcane but never had the "gift". He was, however, very good with computers and programming, so he made his persona in the Matrix that of a mage, complete with wizard hat and robe. All his attack programs were coded as spells. His name was Merlyn, The Magician of the Matrix.
The team consisted of a real mage (Trinity) and a Street Samurai type (Wings) who had cyber-wings installed (modeled after Archangel from Marvel comics, except not blue skinned) which allowed him to glide, but not actually fly (he had an upper floor apartment in a high rise in Seattle). Merlyn was probably cybered MORE than the Street Sammy... I think he had .2 ESSENCE left with all his upgrades over the years.
Anyway, fast forward to today. We've picked up the SR4A edition and have created new characters to run with. However, I'm in the process of also updating all the original characters to use as NPCs. Meryln was caught in the Crash of '62 and survived. He also was the richest team member (always skimming a bit off the top of every run). After the Crash, Merlyn felt the need to get himself out of sight, out of mind, and he needed some MAJOR upgrades, because as technology advanced, so did his desire to acquire it. He wanted a complete transformation, so he decided to start completely over... to put his body back to baseline health and start from scratch! Using a great portion of his wealth, Merlyn underwent three major treatments: Age Rejuvenation, Augmented Healing, and Revitalization. His intention was to remove all his old cyberware and restore his natural body in order to eventually upgrade EVERYTHING inside him by replacing all his old stuff with the height of current technology and quality.
To better prepare his body, he underwent the Leónization process first. This would give his aging body a much greater capacity to heal for the upcoming surgeries. The process worked flawlessly and he came out looking and feeling like he did when he was 21 years old. Next, he had all his old, dated cyberware systems removed and immediately began the Augmented Healing process which would regenerate his meat body to full health and ability. He noted how strange it was existing with no cyberware after having been 'enhanced' for the majority of his life. In some ways it was liberating being fully human once again. Still he felt empty and cut-off from the Matrix he knew and loved, so as he began the last phase of his plan, the first thing he did was buy the top-of-the line Fairlight Caliban comlink with Simsense and Nanopaste Trodes, and then commenced the process of upgrading it himself and writing software for it. At least this would give him something to do during the long months of the Revitalization process.
This is where everything got really weird!
Normally, Resonance/Magic cannot be restored using Revitalization, but as Merlyn's Essence slowly returned, he found that he was gaining even greater insights and abilities in the Matrix. Chocking it up to becoming a "whole person" once again, he gave little more thought about it until one day months later (after spending a few hours dealing with his affairs in the Matrix, visiting old friends, and doing some "general exploring") he looked down to find that his comlink had been off the entire time!!! He had been in full VR for hours without a comlink, simsense, or trodes! Upon this realization, his abilities flared to even greater heights and his vision opened into a deep, deep resonance level. He had just immediately and spontaneously undergone SUBMERSION (the Technomancer's version of Initiation)!!
So now, unbeknownst to anyone but himself, Merlyn is actually a Technomancer, a ghost in the machine, a master of the Matrix. Trinity, Wings, and the rest of the gang as well as his children do not yet realize this, as he has become more of a hermit/recluse and usually stays in contact with them through the Matrix rather than face-to-face (he's become slightly more paranoid as time goes by and is still exploring the extent of his new found abilities, so enjoys his physical solitude). He wears a digital mask that shows him as his 'old' self when communicating with his old friends and family, but he is quickly creating a new persona and name for himself with the younger generation, too, now. What he likes most, though, is how the power sings through his very soul bringing him as close to a real mage as he has ever been before in his life!