Lorraine Shepard and her team found the ship's crew trapped in strange capsules. There, they witnessed the horror that was unfolding. The collectors had been abducting humans to process them into a Reaper. Shepard managed to rescue the crew and all the humans they could save. Tali was sent to accompany the survivors back to the Normandy while Shepard sets up her team to infiltrate the chambers filled with seeker swarms.
Unlike the first operation, the second op went without a hitch. Without Jacob, Shepard pinned much of her operation on Garrus. She was pleased he could get the job done. As they planned on what to do next, the collector forces were gathering outside, ready to breach and attack.
Lorraine wasn't going to stop now no matter how bad the odds were. She picked Miranda and Mordin to accompany her as they found the Human Reaper the collectors had been constructing. Killing Sovereign made humans the target. The Reapers were likely trying to understand how could Shepard accomplish all the things that she set out to do. Harbinger was about to find out first hand.
Lorraine destroyed the human Reaper construct and proceeded to set the charges on this place. The Illusive Man attempted to persuade Shepard to keep the place, but Shepard refused to listen. After everything that had happened, Lorraine had significant doubts over what the Illusive Man would do to this base. Deep inside, something else drove Shepard to this decision.
Shepard didn't want to remember this place and all the men and women she had witnessed liquefied for the Reapers' purposes. Furthermore, she didn't want to remember that she was responsible for Jacob's death, just as she was responsible for Ashley's untimely demise. Miranda supported her firm decision, choosing to leave Cerberus for good.
The collector base was crumbling fast and its collapse almost claimed Shepard and her team's lives. With great haste, the team fled for the Normandy while being chased by the collector forces. Whatever it was Harbinger hoped to learn about the extraordinary capabilities of Shepard and the humans did not materialize. With no plan against the humans and no other resource to tap, the Reapers had no choice but to strike the Sol System and crush the threat that had stopped Sovereign and the Collectors.
Shepard faced the Illusive Man, their differences becoming a driving wedge between the two.
Thane attempted to ease her pains, recognizing what it meant to lose someone she cared for. He helped her move on and grew to care for her. Lorraine for a time felt the same for him, but realized that his terminal condition would make her relive the same horrors she went through with Jacob. They were simply not meant to be.
Instead, Shepard approached Garrus, one who she could trust and wouldn't crush her like Kaidan did.
Shepard knew the Reaper invasion was coming and that she needed to do much to prepare the galaxy. She decided to go back to Earth and reach out to the human council. It was time everyone heard the truth they all hid from.