Operation Scalpel

Operation Scalpel was the name given to the highly classified effort to save Commander Shepard after she was discovered in the depths of a fallen reaper.
=== Discovery and Retrieval ===
On December 10th, 2186, three days after the firing of the Crucible, Private First Class Douglas Einarson discovered a Reaper that had crashed in the city of Birmingham. As he approached, his omnitool picked up a signal coming from the crashed ship. He quickly reported back to his officer, First Lieutenant Karissa Skyler. Within an hour, they contacted Admiral David Anderson and began the prep-work necessary to attempt to isolate the signal so they would have a starting place to try to cut their way in. The group's tech Corporal Willemer made some adjustments to their scanner which slightly cleaned up their data, but the readings were still diffuse. While Einarson continued to try to isolate the signal the following day, Anderson suggested he try to match the spike they were occasionally reading to 1688 megaHertz- a hunch the private confirmed. Two more hours later they were able to approximate location of the spike. It took two after that to find something to cut through the Reaper's hull. Anderson explained to Skyler that the signal matched a small KIA transmitter that the Alliance was rolling out for testing- and Anderson knew Shepard was wearing one.
Late in the day on December 11th, the crew cut far enough into the Reaper to discover Shepard's comatose body encased in Reaper tech and attached to the ship. Further, anyone who touched her experienced intense visions. After Einarson accidently touched Shepard due to his exhaustion while guarding her, he saw first a vision of death and pain then one of hope and life. He awoke several hours later, feeling calm and well rested, remarking to Anderson that he felt very Zen. This reminded Anderson of the quarian Admiral Daro’Xen vas Moreh, who despite her somewhat callous attitude towards both organics and synthetics was nevertheless a genius when it came to synthetic workings. On the 13th of December, Xen, Anderson, and Hackett met together deep inside the fallen Reaper to try to come up with a plan to safely remove her. After some time discussing the issue of not knowing what was safe to cut due to the diffuse readings all around them, Lt. Skyler suggested that they figure out some way to send Shepard a message. When queried on how they might do that, Xen suggested that the geth might be able to communicate with Reaper systems and thus Shepard herself. After searching though a large warehouse where the shut down geth platforms were being stored, Xen located a "sheepdog program" designed to safely collect memory dumps from other processes, shut down any that aren't responding, and reroutes all of the rest to central data storage. Using this program, they were able to "condense" the life signs coming from the ship to the immediate area around Shepard herself. Using the life signs as a guide, they carefully scanned and cut where there were no life signs until the managed to free Shepard along with a not unsubstantial amount of Reaper tech from the Reaper itself.
=== Pregnancy ===
On December 15th, after being cut from the Reaper, Shepard was transferred to the SSV Parigoria hospital ship into the care of Dr. Emma Fallujah. The doctor was chosen due to her being the Alliances top cybernetics specialist, and Shepard appeared to be fused with the machine in places. An extreme complicating factor was that Shepard was also pregnant. It took about week to discover that the embryo was not human (as the Doctor would later testify “It wasn’t exactly the first thing I thought to check," ) and more time to discover the DNA of the fetus was turian. Once the species was identified, they quickly narrowed down the father to Garrus Vakarian. Unfortunately, Garrus was among the missing, having been on the Normandy trying desperately to get beyond the Relay per Shepard's orders relayed via omni tool when the Crucible went off. Not having a lot of data on turian neonate care, they reached out to Garrus' father, Aelianus Vakarian. On January 8th, the day after Dr. Fallujah made contact with Aelianus, the Praetor reached out to his old boot-camp friend and Citadel Councilor Sparatus Calidian Lexios and requested help in acquiring paracetimium acholinisterase alpha- the levo equivalent of something necessary for healthy turian pregnancies, telling him “Sparatus, I’m going to become a grandfather.”
=== Impending Fatherhood ===
It took four months for the Normandy to be repaired enough to be space worthy again and another month to reach the mass relay. After Tali'Zorah was able to reactivate the Exodus Relay after some creative programing and the Arcturus Relay a few days later- after some calibrations. Once the Normandy limped her way into port at Terra One in geosynchronous orbit above Earth, Hackett told Kaidan Alenko and Garrus that Shepard was alive, sent Kaidan on his way, and directed Garrus to speak to his father. Aelianus brought Garrus to see Shepard and explained that he was going to be a father. After discovering a strange "pull" coming from Shepard, Garrus reached out to Anderson for a sanity check, then got in contact with Miranda Lawson due to her extensive experience with Shepard due to heading up the Lazarus Project. Due to the lack of progress on safely removing the Reaper Machinery on Shepard, a contingency plan was put in place: if Shepard went into labor without them finding a way to remove her from the cocoon safely, they would attempt a caesarian with whatever tools necessary and while they would try to save both, they would "Let Shepard Rest" if they were forced to choose.
=== Special Delivery ===
Shepard went into labor on September 20th- a few weeks ahead of when they expected her due date. They became aware of her active labor when Shepard projected her screams through the intercom and other computer systems. Ann Joyal, one of the nurses monitoring her care, was extremely disturbed by this development, later testifying " . . .(the scream) wasn’t coming directly from her, but it couldn’t be anything else. I just knew. I could feel her— it was like she was everywhere all at once. Sometimes it honestly felt like the sound was coming from inside my own head.”
Miranda and Dr. Fallujah prepared to perform the c-section, but not only did Shepard regain consciousness but also the machinery detached on it's own- it's job presumably finished. Though she was dehydrated and more than slightly worse for wear, Shepard was able to successfully deliver her daughter with the support of Miranda, Dr. Fallujah, and Garrus.