In the Mass Effect universe, the dead won't always stay dead. Commander Shepard gave the extinct Rachni race another chance on Noveria, then the Commander got a turn.
Mere weeks after the battle of the Citadel, the Normandy was patrolling space when a massive, unidentified cruiser intercepted it and opened fire. It was the Collector ship, and the Reaper-affiliated Collectors wanted Commander Shepard (Sovereign's killer) dead at any cost. Sure enough, the Normandy was blown out of the sky, and the Commander was killed in action, no questions asked. But that wasn't the end.
Race for the Body
The Commander's body was a wreck, but it wasn't blown into space dust. There was enough of it leftover for various parties to take an interest, and that includes Cerberus and the Collectors themselves. The Collectors wanted to study their greatest enemy, while The Illusive Man simply wanted humanity's greatest hero back on the scene. Liara T'Soni, a loyal ally of Shepard's, soon entered the picture as well.
At first, Liara was working with the Shadow Broker alongside a Drell agent named Feron. The body was indeed recovered, but the Shadow Broker moved to have it gifted to the Collectors. Liara couldn't accept that. She and Feron risked their lives to steal back the body, and Feron ended up in the Shadow Broker's cruel grip. Liara swore to save Feron one day, but for now, Shepard's remains needed her the most.
While Liara is hardly an ally of Cerberus, she trusted them more than the Shadow Broker or the Collectors. She willingly passed the body and its capsule to Miranda Lawson, though with slight misgivings. What if Cerberus poked and messed with the body as the Collectors would have? And shouldn't Shepard get the chance to rest in peace? Ultimately, Liara allowed Miranda to do as she willed. It was time to bring the dead back, and not a moment too soon.
Rebuilding the Hero
In life, Commander Shepard wasn't on friendly terms with the ruthless and shady pro-human cabal known as Cerberus, but now, Cerberus was the only party interested in bringing the Commander back. The Council was powerless, as was the Alliance. Meanwhile, The Illusive Man was ready to empty his coffers to bring the Commander back to life. He created the Lazarus Cell to that effect, placing Miranda in charge. Two years and four billion credits later, the Commander's body was rebuilt, from the bones to the muscles and blood, and, most of all, brain functions. Many advanced cybernetic parts were added to keep the Commander's body together and keep it running, but the Commander was not a full-blown cyborg. Most importantly, the Commander's brain functions were not altered.
Miranda wanted to add a control chip to Shepard's brain to more easily control them, but The Illusive Man objected, stating that he needed a perfectly original, unmodified Commander Shepard, just the way they were when Sovereign was defeated. Reluctantly, Miranda finished the project on her boss's terms, and the Commander was ready to fight.
Other modifications were possible, however, with the influence of game mechanics. The player can choose to alter their Shepard's face and powers if so desired, since the Lazarus project is reconstructing the Commander from the ground up. It's possible that a mere soldier has been reborn a biotic, for example, and with a new face, too. At any rate, Shepard will retain all memories from their past life, from the battle of the Citadel to personal romances and beyond.
Miranda was rather cautious about the Commander when they came back to life, since the Commander hadn't been terribly friendly toward this rogue extremist group. Jacob Taylor, by contrast, is more neutral and welcoming, and he understands perfectly if Shepard is still making up their mind on whether to trust Jacob and the others.