They weren't given any time after that to really be together - EDI awoke her at 0600 at the behest of Admiral Hackett requesting admittance onto the Normandy SR-2. Shepard nuzzles her sleeping Turian, kisses his lips softly, before rolling out of the bed to slip into her normal casual Cerberus fatigues, though she made sure to tear free the Cerberus patches the first chance she had. She alerted EDI to allow Hackett onto her ship, striding from her quarters to meet Hackett in the CIC. They salute, and retreat to the comm room for a private discussion from prying eyes.
------
They emerge an hour later and Shepard calls the entire crew to the CIC, save Joker who remains informed through an established comm link with EDI. Shepard levels her gaze with Garrus for a brief moment, an almost apologetic expression bearing before it slips away to as she stiffens her posture, folding her arms behind her back to address her crew members(all of which had actually showed, even Jack, and Thane, Grunt - that surprised her - as well as every Cerberus crew member, which was also a touch surprising, but uplifting).
"It has been an honor to serve with every one of you. I have agreed to surrender the SR-2 Normandy over to the Alliance from this moment forth. All previous Alliance crew will be returning to Earth with Hackett and I - the rest of the crew will be granted immunity and shall disembark on the Citadel, or return to Earth by choice of surrendering yourselves over to the Alliance, same as I."
The room was quiet for a long moment, then Gabby and Ken share a look before stepping forward to salute Shepard and Hackett. "We will go back to Earth and the Alliance with you, Commander," Ken declared. Chakwas, Kelly, Joker, and a number of the Cerberus crew all agreed as well. It surprised the hell out of Shepard to see Jack agree as well, even Jacob. Miranda was, unsurprisingly, silent. None of the others seemed to have nothing to say, all watching her with a different range of expressions.
"Very well." Hackett nodded. "Joker - set a course for the Citadel."
"Aye aye - sir. ETA 10 minutes."
Shepard turned and shook hands with the Admiral. "I won't toss you in the brig, Commander, but you will - for appearances sake - have to be confined to your Quarters. Say farewell to the crew while you can...and I am sorry about this."
"Don't be, sir. I understand."
------
They docked at the Citadel and after a number of goodbye's, Shepard was left standing in the CIC with Garrus after the rest of the crew had disembarked, save for the ones returning to Earth with her. A human man, Vega, had come aboard the Normandy and was standing in the cockpit with Joker, cracking jokes as far as she could hear.
"Well...this is it, I guess..." Shepard shrugs and then says ah, fuck it, before she wraps her arms around Garrus, laying her head against him. "I will do everything I can to keep in touch and never doubt that I'll come back, Garrus. I...I won't let anything stop me, and I am sorry I have to leave for a while."