Any history of June Shepard must begin with how little we know of her. We do not know her parentage or her birthplace, and much of her active history remains classified. We know that she enlisted in the Systems Alliance military at the age of 16. Her rise through the ranks was as meteoric as it was inevitable. Despite occasional reports of insubordination, her talents could not be denied. She became an N7 marine at age 18, and on her first mission was deployed with her unit to investigate distress signals from Akuze, an outlying human colony. Unfortunately, the distress signals were imprecise; her unit was sent into a nest of thresher maws, and only June survived.

The details of her survival remain classified. It can be assumed that she acquitted herself well, because the disaster on Akuze did not stem her ascent through the ranks. Two years later, she was XO of the SSV Normandy on its maiden voyage, a supposed shakedown run to retrieve a Prothean artifact from the colony of Eden Prime. It was at this point that the star was firmly affixed to her brow. Far from being a shakedown run, it turned out that Eden Prime had been invaded by the geth. Shepard and her assistants Mortimer Halliwell and Suzanna Shi cut their way through the geth forces, discovered that the invasion had been instigated by Spectre agent Saren Arterius, and interfaced with the Prothean artifact, receiving an ancient message: that the Reapers, a race of biomechanical monsters, had destroyed the Prothean civilization and would come for the current civilization as well.

Shepard went to the Citadel Council to inform them that their agent had betrayed them. They refused to listen until she found conclusive evidence of Saren's betrayal - in the form of a geth data core salvaged by Quarian machinist Sal'Poma nar Marvan, which had recorded Saren plotting with his compatriot, one Matriarch Belara. Along the way she recruited C-Sec officer Garrus Vakarian and Battlemaster Yakhol Warhead, both of whom would have their own parts to play in the coming adventure. Shepard returned to the Council, proof in hand, and for her efforts, was made a Spectre and given her first mission: to apprehend Saren before he could execute whatever terrible plan he had in store.

Shepard's first order of business was to rescue Belara's daughter, Arela K'Bael - initially in case she was a co-conspirator with her mother, but while it turned out she was not, her expertise in prothean civilization and her biotic prowess proved very useful. She then traveled to the colony of Zhu's Hope on the planet Feros, which Saren had mysteriously visited a few weeks prior; there she found an ancient life-form, the Thorian, which helped her to clarify the vision she had received from the beacon. Finally, she traveled to Noveria, chasing down Belara herself. The matriarch turned out to have been breeding rachni, the insectoid creatures against whom the Citadel had fought a desperate war two thousand years prior. When defeated, Belara revealed that Saren had been using a subtle form of mind-control on her, which she referred to as "indoctrination". June was then faced with a choice between killing the rachni queen for the crimes of her ancestors, or releasing her to potentially war with the Citadel races again. She chose to release her.

After Noveria, the Council contacted Shepard with information on Saren's activities. An out-of-the-way planet, Virmire, had sent a distress signal indicating his involvement. Shepard was sent to investigate. There, she found a cloning facility, breeding an army of krogan shock troops. Shepard infiltrated the base, coming into contact with Saren's flagship, Sovereign and making the discovery that it was, in fact, a fully sentient Reaper - and that the "indoctrination" Belara had spoken of was affecting Saren himself. Shepard set up a nuclear device to destroy the cloning facility, and following a confrontation with Saren, made it out unscathed. Saren's next goal was to reach "the Conduit" on the planet Ilos, and thereby to summon the Reapers. Shepard was fully prepared to follow him into the Terminus Systems and defeat him.

Unfortunately, the Citadel Council had other ideas. Sending one ship against Saren's fleet would be suicide; sending a fleet into the Terminus would be an act of war. They locked down the SSV Normandy and confined Shepard to the Citadel until further notice. Fortunately, Shepard had the assistance of her former CO, David Anderson, and the human ambassador to the Council, Donnel Udina. With their assistance, she released the Normandy and chased Saren to Ilos, in an act of full mutiny, while they gathered the Alliance fleet in Citadel Space and prepared for an attack from Saren. There was no turning back now.

On Ilos, Shepard discovered a Prothean virtual intelligence, which told her more about the prothean extinction: they had been sabotaged by the Reapers, who used the Citadel as an enormous mass relay to bring them from deep space into the perfect position for an invasion. However, Ilos had housed a small team of scientists, who used their expertise to create a miniature relay to the Citadel and sabotage the Citadel itself. It could no longer be automatically activated by the Reapers, but would have to be manually engaged by Saren - who had, by now, used the scientists' relay to enter the Citadel undetected, and signalled his fleet to attack. Shepard followed Saren through the relay and battled her way through his army to the Citadel Tower, where Saren was in the process of engaging the Citadel relay. She defeated him, disrupting Sovereign through its connection to him and allowing the Alliance fleet to destroy the Reaper while its shields were down. The galaxy was safe - for now.