Shep can't leave at any time physically or even in the possible sense. Miranda is there to make sure he stays tied to Cerberus she's the real commander not shep. She also has cameras to catch him in the act and she reads all his emails shep can't leave or message for help or quietly plot with his friends because Miranda has access to it all and if she does do do others she can't possibly work 24/7 on spying on shep. We also have Kelly and EDI who help to spy on shep and keep him chained to Cerberus. So no we can't leave, we should've been able to as a poster suggested a long time ago shep could say FU tim storm out of the base go to the Alliance get turned down then go to the Council and get turned down by them then have to come back to TIM if he wants to keep the plot rolling if the player isn't ready to do that they can just hang out and do whatever but the plot won't move forward until you go back to TIM.
TIM keeps shep isolated by not allowing him to contact his old friends who weren't approved by Cerberus Shep also makes no effort to contact them one could say thats because Miranda would've stopped the email or jammed the call but players can't do anything to attempt to reach them. More railroading
For the LP there is not only tons wrong with it but also loop holes created with it!
Shep's body "servived" planet reentery ie burning up and it "survived" smashing into the icy ground below sorry even if it had the gravity of the moon the body would still be dust.
However Liara's comic retcons this physical fact we see a chared shell shep but wait the planet itself retcons her comic! The helmet and the chest plate were found on the world. Legion says he found part of your armor and repaired himself with it and you yourself find the helmet. Liara also has your chest plate and chared shep was naked so all this implies somewhere between the SB and Liara someone striped him ripping the armor off and somehow doing that with a fradgile corpse didn't break more off? In the opening X-rays we see shep has lost part of his leg below the knee. You unwrap a mommy wrong and the whole thing will snap and I'm suppose to believe they could strip shep load him into a cryo tube and he's ok?
Brain damage sorry dead for 2 years = shep's dumber then a rock if you go over the 1 minute mark and you're revived your risk of brain damage, nerve damage, or cellar damage increase tremendously so shep wouldn't be perfect upon waking up.
The only way to fix said brain damage is to plug shep into a reaper husk maker we know those things can correct such issues via them not caring about the gaping holes in their chests but we also know they're only aware of so much basically they have zombie syndrome.
There is no ingame evidence of any other technology available to recharge and fix shep and TIM's secret closet of technology isn't evidence its blanket argument if we don't see it or read it in the books you can therefore say it doesn't exist and isn't available in the world unless BW wants to do what they did with the endings and cram a round peg and a square hole and hope people don't notice. If they can fix death they can cure Miranda and Jack oddly they don't. The only death solving tech open is reaper based and made.
Clone shep makes more problems once real shep was up a running why didn't TIM destroy him? How is it Miranda didn't know about him? She was head of the project we're expected to believe that the head of the project didn't know about the clone they were using as spare parts? We also have the problem of Shep was the only test subject so does that mean clone shep was that test subject? Or was real shep that test subject? We have no evidence.
Cerberus shows a history of testing touchy techniques on other people in order to protect their primary test subject see Jack for this real shep was Jack 2.0 and clone shep was all the other children 2.0 yet Miranda didn't know this but Jacob kind of knows?
Why wake up clone shep? Maybe Brooks did it but if real shep's people couldn't find him how was Brook able to find clone shep? Why wasn't clone shep guarded and monitored? Why grow a full body when all you needed were the parts? I can grown arms, liver, eyes, ect and keep them suspended in solution I don't need a brain or spine because if my patient needs a brain or spinal cord he's way to gone for me to work with.
Did we have two ships? How does clone shep get around? Did clone shep get a brain chip? How did TIM know this chip would interfere with how shep was unless they gave it to clone shep woke him up and tried it out?
How did they give shep his memories? How did they know it was going to work? Was Liara brought in to help with this? Outside of LI shep how would she know info on Tali's pilgrimage gift, or other important shep only things? Are we to believe that Liara was melding far deeper then she said in ME with shep?
What about shep's psychological state? HE DIED that effects everyone whose ever returned from that state they're never the same yet TIM thinks shep would be? No treatment just day one up off the table get to work? What if shep had a break down during the mission?
Shep had glaring weaknesses hacking, weaknesses to emp and Miranda, Wilson , or TIM didn't foresee this? And after all that happened there were no patches done? These two things alone make shep a walking liability and yet they make him the spear head of their operation in ME3. Miranda just seemed to "forget" about the fact reapers can hack reaper code?
Shep has reaper code yet no reaper parts? Really we're expected to believe this? EDI is made from reaper tech the metal in shep's bones, the nodes, the enhanced eyes, his fake skin yet I'm suppose to believe none of this is reaper based? Just because it doesn't indoctrinate doesn't mean shep isn't made from reaper everything the most advanced civilization is the reapers you can't even say the protheans are because they were dependent on reaper tech fully.
Shep's viability in 3 they keep saying how shep would make a great parent but can shep even have kids? Like everything else after 24hours of death everything breaks down even if you keep them on ice or cryogeniclly frozen there is cellar damage even sperms or eggs must be disguarded from donation centers after a point because the samples are too damaged so can shep even have kids? If Cerberus thought this was something else they needed to fix why didn't Miranda sign up for it too?
BW has done nothing to explain the LP or improve upon us understanding it they simply gave us 3 videos in 3 that rehashed what we already found in ME2 shep was dead, it was next to impossible to bring him back, yet somehow they do and he's fully functioning and aware, time to fight the collectors....
So far the games themselves are doing a better job of showing us what probably went into shep:
Sanctuary looks like a direct pull from what they learned between David, Shep, and Grayson they could fully control how many, what types, and how smart their reaper thralls were they could make solider class like their cannon fodder or husk banshees there wasn't any limit to what the could achieve.
The various reaper making devices around dragon teeth are amongst the most popular however they aren't the only ones back in ME they've found small things that indoctrinated that then prompted the thrall to make their friends into husks. These kill, break down the organic cells and replace them with electronic cell like things and they reanimate the dead into conscious beings they may have low intelligence but they're back, kicking, and fallowing orders. We know after the reapers leave the husks display some sense of intelligence however they refuse to do anything to help themselves and slowly starve to death.
We know there is not cure for sterility see Miranda clone or not it would be fixable if she found away during the LP.
Clones have genetic markers making them obvious to those who know what to look for so clone shep can't be real shep the scanners would know, the doctors would know.
AI and humans can be combined see David so its possible shep is an AI but again no ingame evidence to support this Legion would at least be able to tell if shep was broadcasting signals and of course when they loaded him into the consensus. Not to mention Lev would've been able to tell.