The only fathomable reason she -would- poison the LW's mom is because Li was envious of Catherine's position as James' wife. She had the hots for Liam Neeson apparently. Even then, Li was massively pissed and felt betrayed when James ditched project purity ~19 years before due to the death of his wife. As you said, nothing really ties Li to being this sort of double agent...

I actually hope that Dr. Li will end up being the good guy behind the scenes. I don't know why, but I always wanted to like her.

I read the entire OP yesterday. I don't know and/or remember enough lore to really talk much about it, and I don't remember too much of what I read yesterday . It's clear a lot of work went into it, nice job.

The one thing that stands out in my memory, trying to connect anything to release dates can be very tricky. Everything else is lore, but of course release dates are affected by all kinds of real world stuff, so just in general I feel like theories about them are much more likely to be wrong.

Again, nice work. I've been reading here for weeks and you put a huge amount of time and effort into these, which is cool.

I'm glad you liked it. And yes, a lot of work went into the thread (something close to 100 hours of research and editing just for this one!)

Regarding your mention of release dates, I'm not sure if you mean the announced release date of the game itself, or the year in which we emerge from the vault. Either way, you may want to check out http://www.gamesas.com/topic/1528530-revolution-216 thread, in which I have even suggested an actual date for the beginning of post-war gameplay!

Note: I have literally just added even more compelling evidence to the linked thread, which further supports my suggested date as being the exact day we begin Fallout 4 after emerging from the vault.

I don't get why Doctor Li is a sleeper agent for the commonwealth.

Yes, that's why Bethesda included the "Vault-Tec?" option when speaking to the rep in the game. If anyone cares enough about Fallout, just joining the series, to be on the forums then they'll probably also have seen the wikia's when google Fallout and will look there. Hell when I was getting into Fallout just before the release of Fallout 3 I went out and bought 1 and 2 but I don't think many people will have done that.

For anyone wondering about the Madison Li angle, here is a full explanation...

Whilst researching this theory, I have tried to view every aspect from a broader perspective, in order to encompass elements of Fallout 3 (and other games) in ways that make sense.

The idea is that Madison Li was born and raised inside the Institute, having come from one of the original bloodlines. Or at least that's what she believes. In reality, which would actually fit the premise a lot better, she may have been 'found' as a very young child by a scouting party from the Institute and made to believe she was actually born there. This would be very similar to the way that I have suggested Shaun was deceived. If this second option is true, then she could even have been found https://www.google.co.uk/maps/place/Madison+County,+VA,+USA/@38.4286389,-78.2677876,9z/data=http://forums.bethsoft.com/topic/1528436-the-mother-of-all-theories/!4m2!3m1!1s0x89b43fa2d4f1e049:0x72bbc41d577e4788, which would explain her name, as well as her'connection' to the Capital Wasteland. (Note that this second option would actually make the Memory Den highly relevant to Dr Li, and not just Shaun as I have suggested http://www.gamesas.com/topic/1527024-jack-and-nora/?p=24160144).

When she reaches advlthood, bearing in mind she would be totally indoctrinated into whatever beliefs and values the Institute represent, she is sent to the Capital Wasteland. Here, using knowledge acquired at what would most likely be the most advanced scientific facility on earth, she establishes herself within the local scientific community. Her mission? To acquire knowledge, resources, and technology for use by the Institute in conjunction with whatever agenda or plans they are currently undertaking. Note that the information I am suggesting here would effectively make the Institute the https://en.wikipedia.org/wiki/Keyser_S%C3%B6ze of the wastelands.

Being of extremely high intelligence, Li would very easily be able to play a role that would 'prove' to others what a good, kind-hearted individual she is, and how much she values the needs of the many. This would also allow her to be accepted into the community to such an extent, that she would eventually be granted access into the impenetrable fortress that is the Citadel. At the same time however, we must consider Dr Zimmer as part of this equation. There are a number of options here. Either Zimmer had never actually met Li prior to his arrival at the Capital Wasteland, or he was 'in on the act'. Or he may have even had certain memories removed or suppressed.

Looking now at Harkness. Perhaps he had information or data in his 'memory banks' that could have caused a problem for the Institute if it were to get out. Especially if this information related to a hostile takeover of not just the Commonwealth, but the entire East Coast and beyond. This would explain not only why Zimmer was so eager to recover his 'lost tech', but also why Li could not under any circumstances be seen as being involved. It would also give further reason why Li could have murdered Catherine, especially if she was close to uncovering information that could potentially affect countless thousands of post-war survivors.

But why, you might ask, would the Institute be interested in taking over the Commonwealth, never mind anything beyond? Because maybe, just maybe, they are nothing like the 'mustache-twirling villains' that they have presented themselves as being. I actually believe, based on all of my existing research, that the Institute are in-fact scavengers, reborn into a post-nuclear world just like everybody else, fighting for their own survival. And that they not only stole pre-war technology, such as the GECK and the nuclear reactor cores I mentioned in the OP, but also people, including Shaun and Dr Li herself. This would actually fit perfectly with the world of Fallout 4, in which everything we find now has value.

And so, in a bizarre twist that would make them seem a lot closer to many of the other factions in the wastelands, including the Brotherhood of Steel, they scour the wastes, looking for people, technology, and anything else that will ensure their long-term survival. And with their latest plan underway, which would guarantee their access to any resources they would require for the forseeable future, to paraphrase a popular saying, ships are about to get real...

No offense, but are we even playing the same game? At no point did Dr. Li express anything other than, ‘I am here to help people.’ She seemed just as passionate about Project Purity as Catherine was, so when James quit it, she obviously got pissed off.

Still haven't answered my question on just why and HOW she'd murder Catherine and get away with it, then break James out of Vault 101 after the game made it empirically clear that James did that himself. Isn't it enough to accept that Catherine simply died due to complications in childbirth?

And really? All this because she grew up in the Commonwealth? So did Sole Survivor and yet he/she isn't conniving a plan to take over everything. Give me quotes that prove she did work with the Institute, because if I remember correctly, she merely grew up in the Commonwealth as a scientist. She had no connection to Synthetic beings, etc. She hated Zimmer because he was obstructing her project to help the people of the Wasteland, to make her team play Wasteland Detective for him on locating some synth that ran off. She wanted no part in that.

Look, I can buy that the Institute probably just wants to rebuild the world their own way, etc. I just don't see how Li killing Catherine or knowing/caring about Shaun would help their plans in the long run. As a matter of fact, wouldn't Li want Catherine and James to join? I could see it now, "After all this is over, would you, James, and your baby like to come with me to the Commonwealth? We're working on rebuilding the world and we could use your help. What do you say?" Catherine might actually be willing to help.

EDIT: OK, I'm going to go turn on Fallout 3 and talk with Li and Zimmer. See what I can find out.

PTSD is a real problem for Vets, and can cause them to go into a kind of weird cross between a flashback and autopilot mode, Also certain pain killers and prescription medications have SERIOUS side effects if cut off abruptly.

Given that the military in Bethesda version of reality was using Psycho and referred to it as a Chem Ration..... heck just being cut off from your Mentats might push someone over the Edge.

Here are my findings after talking to Zimmer and Li:

-> Li had worked with Catherine and James for several years until Catherine died. When James left, Li had nothing left so she went to Rivet City and created the science lab we see in the game.

-> Zimmer pesters Li and her team, pissing her the hell off. She hates that he's distracting her and her team for making real scientific progress in saving lives.

-> Catherine died from complications in childbirth, something none of them were really prepared for. The tapes found in the Memorial tells us that they could never make it past small-scale tests due to issues with the mechanism and other, external, issues.

IIRC, later on when James talks to her, Li has to be convinced that Project Purity wasn't some failed dream, that it could really work this time. Also, IIRC, Li has no idea what the GECK is. If she knew, don't you think she would've mentioned that to James when they were working on the project? Lastly, wasn't she surprised when she saw James again? If she had broken him out of Vault 101*, she would have expected he'd come running to her.

* This implies she knew that James was in Vault 101. How? Where are the quotes to prove this? For all she knew, he was in the Republic of Dave for 19 years raising Lone Wanderer. If she were going to break him out of somewhere, the first thing she'd need to know is where he is at all.

And no, the fact she said, “Aren't you supposed to be in the Vault? James said he left you there.” doesn't support that claim. The implication, to me at least, is that James told her he was at Vault 101 all those years, and he left you there. Then when you show up, she wonders why and how you got out of Vault 101.

So, sorry OP, but Li isn't an evil sleeper agent for the Institute who murdered Catherine, waited 19 years, then busted James out of Vault 101. She was a minor character in a stand-alone game.

To help explain this, I will use an example that's close to my own heart, or at least my own Avatar.

In the movie "Taken 3", we see Brian Mills once again use his very particular set of skills, but this time he has been framed for the murder of his ex-wife. The only clue we have as to the identity of the main villain is something of an 'unusual' change in the casting line-up. To cut a long story short, the new husband, who was portrayed as a 'good-guy' in the first two movies (he was a successful businessman, but also seemed a bit 'flimsy'), was actually behind the murder. Why? Because he managed to get on the wrong side of one of his not-so-legit business contacts, and ended up owing a huge sum of money to some very dangerous people. Cue the inevitable 'life insurance' plot twist, add in the framing of the ex-husband, and you can pretty much see where this is going.

Now, I'm not saying that was the best plot in the world, but it was still a fun movie. Looking again at Madison Li, if you wanted to set her up as a recurring character, especially one who could end up as a future antagonist, one way of doing this would be to present her in a particular light (in this case as a good, 'no-nonsense' doctor), but to leave subtle clues that could suggest otherwise upon reflection, but that many people would not see, effectively making it hidden in plain sight.

Now, there is some additional evidence that I will be posting up regarding Dr Li. But in the meantime, assuming you did have a reason to suspect her, and that she genuinely believed she was born in the Institute, then the others who work and live there would not be mere work colleagues. They would be considered her family. And a very strong theme we have seen more than once in this series is protecting the interests of your family at all costs.

I will be back a little later to post up a few more answers

Well, here goes:

• Reference to Fallout Shelter in the FO3 trailer was interesting & I can see it now. I would like to play this but I have a 4S and it is not supported.
• Factions in FO4 - this is great if they are anything like factions in FONV
• New craftable explosives? I'm all for that. The amount of info from the fridge is amazing! Kudos to the person who found that (was it you and some else?)
• The Blue Star chip thing: it might be a cool Easter egg?
• Philadelphia Experiment: that is interesting link, if true, I wonder how that might apply to the story? If this is what you implied, great sci-fi stuff. I could really get into that.
• Shaun believing he is a synth: mind blown!
• The Institute: I like the idea of them being like another wasteland scavenger. Bad guys on par with Keyser Soze (read the link, never saw the Usual Suspects) ? Yikes!
• Last but not least: Madison Li. It has been a while since I've played FO3, a few months. I will probably revisit with my last character Judith and check some things out for myself. I always got the impression that she really cared about James and may have even been a little jealous of Catherine. Not sure if I go along with the part about murdering her just to delay Project Purity, I hope not? I know Anna Holt turned out to be a traitor. But Madison - if she worked for the Enclave (and Institute) why did she help the BoS with Liberty Prime (or did I miss something)?
• In any event, I had a feeling that we hadn't seen or heard the last of Dr. Li when they said she headed north to the Commonwealth.

Wow that is quite some bit of detective work, new stuff included, and I have to say I'm impressed. Even if HALF of it turns out to be true, you have earned a place in the Fallout hall of Fame. Great job!

edited for clarity

Starting with the Dr Li theory.......I'd say that would be a major re-writing of the character, her decision to head to Commonwealth makes sense since the Purifier isn't under her control and her Rivet City project has largely been made obsolete by the pure fresh water.

We do not know I believe where she or James were from originally just that they came to the capital wasteland and established project purity along with other scientists, I'd suggest that they were probably from the Institute since its the only scientific group we know about on the east coast.

So we can I suppose theorise that perhaps James, Li and the others were sent to DC (or left voluntarily) to prove that their project to mass purify irradiated water would work and once the project was successful Dr Li returned to the Institute in triumph with some hugely important technical knowledge. There is no real need for her to be secretly plotting since her team of scientists probably all came from the same place at least initially and there is no reason she wouldn't be free to return to the institute once the project was successful.....at least until James screwed his colleagues over.

I do think Dr Li will play an important part in F4, perhaps as a faction leader within the Institute.