Something REALLY important.
"I noticed a few upgrades", said Shepard, "I hope you didn't replace anything really important"
"We tried to keep you as intact as possible", replied TIM, cybernetic eyes glowing, "We need Shepard, just as you were when you defeated Sovereign".
Shepard struck back, "What are the reapers doing that made you decide to bring me back?"
"We're at war. Nobody wants to admit it, but Humanity is under attack...
I'm not sad that's over, thought Shepard as he exited the comm room, though it does make sense...
"Shepard!", called Miranda, "We're leaving in fifteen minutes. Your weapons are in the Kodiak."
Shepard was about to move towards the shuttle, when a familiar urge, well, urged him.
"Miranda, there any bathrooms here? It's been a couple of years, and I'm bursting"
"Second door on the left" she quickly replied.
"Thanks", Shepard said back.
Ahhh, though Shepard, gotta be the longest pee for a few years now, though something feels odd...
He looked down. What he saw more than surprised him. It astounded him, confounded him, and confused him. They DID replace something really important. Not complaining though... Ashley, here I come!