I know the TOR project was started by the US navy, and that now I2Pnis the preferred method of browsing the darknet, because many people believe it has been compromised.
> and that now I2Pnis the preferred method of browsing the darknet
This is not true by any means. A "switch" to I2P never happened, and just a few months ago an exploit[1] that could deanonymize eepsites was published. Tor is still the only "method of browsing the darknet"; by most definitions.
In the same manner that parts of the NSA are interested in secure cryptography as opposed to breaking it, parts of the Navy were interested in anonymizing traffic as opposed to de-anonymizing.
The TOR software is likely no more compromised than GNU/Linux generally -- the TOR _network_ is likely compromised by flooding it with honeypot servers that can track users by monitoring origins and destinations.