The Mysterious Figure is an individual who hires a mercenary group to assassinate Commander Shepard whilst the Normandy crew is docked on the Citadel for shore leave in 2186. This person takes a particular interest in stealing Shepard's identity, and hides behind voice and visual disguisers to protect theirs.
The Mysterious Figure eventually reveals itself to be a clone originally created by Cerberus to provide spare organs and limbs for the real Commander Shepard, who was being revived by the Lazarus Project.
At some point in its development it was stored in the Minuteman Station, skinless and under life support. Once Cerberus obtained Shepard's Spectre dossier the Illusive Man deprioritized the clone project and allowed project overseer Miranda Lawson to continue using it for testing.
Sometime in 2184, the order was given for the clone's termination. Agent Rasa had other ideas and decided to liberate it from Cerberus hands. A violent shootout at Lazarus Research Station resulted in Rasa severing ties with Cerberus and escaping with the clone's tank. One of its known hiding places was Rasa's old stomping grounds on an asteroid orbiting Themis.
The clone remained in storage until six months before the Reaper invasion in 2186, when it was awoken by Rasa (then known as Maya Brooks). Over the intervening months during Shepard's incarceration, the clone learned "how to be human" with the help of neural implants, and with Brooks' help devised a plan to kill and assume the role of the Commander in order to carry out a pro-human agenda. To accomplish this, the clone hired the CAT6 private military corporation to eliminate Shepard and his/her close allies, since the clone lacked the original's memories, thereby unable to perfectly impersonate the Commander.
Mass Effect 3: Citadel
Shortly after Cerberus' attempted coup on the Citadel, the clone implements its plan while Commander Shepard is ordered to go on shore leave. It purchases arms for its CAT6 troops via arms dealer Elijah Khan, hacks databases to steal Shepard's classified files, and sets a trap at a popular sushi restaurant in the Silversun Strip with the intent of obtaining the Commander's Spectre code.
The clone successfully obtains the Spectre code, but the original manages to escape being killed. To compensate, it uses Brooks to tie up loose ends by having Khan executed then luring Shepard and friends into another trap at the Citadel Archives by intentionally using the Spectre code to get itself and its mercenaries in.
Donning CAT6 armor and pretending to hold Brooks hostage during a clash between its troops and Shepard's team, the clone finally reveals itself and shares part of its life story and motivations. It puts up a signal blocker to intercept any transmissions, and manages to obtain the Normandy SR-2's command codes in the process. Impersonating the real Shepard and comming Samantha Traynor to get the Normandy prepped for emergency launch, the clone orders its mercs to execute Shepard and friends and moves forth deeper into the Archives.
Shepard and team thwart the kill order, but the clone's plan to have them all sealed within the Archives' iridium vaults ultimately becomes successful. Before trapping Shepard and their squad in one of the vaults, the clone and Brooks now reveal the full extent of their plan. The clone makes a show of pointing out that handprints can't be cloned, and promptly updates the Commander's records with the clone's own biometrics before setting out to be captain of the Normandy.
The trap doesn't last for long, and Shepard and friends soon resume the chase. The clone, meanwhile, has been busy taking over the ship: it fires Traynor for "fraternization"/"conduct unbecoming", and disposes of Shepard's cabin accessories in a big bin. Upon learning that the real Shepard has successfully boarded the ship, it leaves instructions for its troops to slow the Commander down, and on Brooks' suggestion heads down the armory to prepare for the showdown.
The clone, now clad in N7 Armor, fights the real Shepard in a pitched battle in the shuttle bay, insulting the Spectre and their squad while the ship is attempting to fly out of the Citadel. Upon learning that the Normandy can't jump to FTL due to Joker and Cortez' interference, the clone dispatches the hangar bay Kodiak to deal with the pilots and continues the assault on the real Shepard's team, not bothering to have the hangar closed.
Eventually Shepard tackles the clone, causing them to tumble down the open boarding ramp and nearly fall off the edge. As they hang on for their lives, the clone demanded to know what made the Commander more special. As Shepard's squadmates, the "emotional baggage" the clone was quick to dismiss, help the Commander up, the clone looks up to Brooks and watches her turn her back.
The Commander is then faced with either helping the clone or kicking it off the ship to its death. If Shepard attempts the former, the clone refuses the original's aid and purposely fall to its death, spitefully asking what it can live for before letting go.
While the clone is an exact physical replica of Commander Shepard, it only has the most superficial idea of what kind of person Commander Shepard is. For example, the clone is intensely xenophobic while the majority of Shepard's closest allies and potential love interests are aliens. Nor does the clone show any concern for the lives under its command (the CAT6 mercenaries), even considering them "cannon fodder", unlike Commander Shepard's fierce loyalty to the Normandy crew. The clone describes itself as the lone wolf Shepard was supposed to be.