Well the idea about the "government theory" is basically:
Maybe I'm insane but here's a possibility: A clear link was established between Silk Road and Mt. Gox. Significant portions of the cold wallet are now frozen. (Yes, the US still has a lot of pull in other countries eg Japan. Think Kim Dotcom. Plus Gox is a registered entity in the United States.)
Transaction Malleability did steal a portion of bitcoins, but not the insane 99.7% amount. Gox is now unable to refill their hot wallet due to the seizure. They are now aiming for an acquisition to cover the funds stolen by transaction malleability, however a gag order prevents Gox from disclosing exactly why the funds are missing, hence for the time being they blame it on Transaction Malleability.
Gox likely had a tiered system of "hot wallet", "cold wallet" and "coldest wallet". It's possible the US Gov took control of the "coldest wallet", which would contain the largest amount.
Gox is possibly now working on some type of 3-way full tilt poker style acquisition deal (Gox, new owners, US Gov) which will result in funds being returned plus a drop in pending charges (which could be sealed).
All pure speculation, but I'm curious as to if you guys can think of anything else that ties this theory together?
http://www.reddit.com/r/BitcoinMarkets/comments/1z2xo5/speculation_the_us_government_has_control_of_goxs/IMO there could be a possibility that this is true. Or maybe I just hope it's true because then the bitcoins are at least not permanently lost.