An idle thought of mine I had recently. I don't know if this has been thought of before, but it makes sense.
We all know that Prothean's can read the experiences of whatever they touch. From the Mass Effect wikia, it says:
A unique attribute of Prothean physiology is an experiential exchange system based on physical touch. By touching something or someone, a Prothean could recall its experiences.
Given how Javik reads past experiences, I'd say it's safe to say all Protheans need to use their hands in order to read something. A biological body would simply be too complex if it was able to read so much data from any point of contact on the skin. Yet when Shepard has that final flashback of Javik's past, Javik wasn't even paying attention to Shepard, let alone touching him/her with his hands. On the other hand, Shepard ended up touching Javik, and only his armor at that. It seems a lot like Shepard was using the Prothean ability to read Javik's experiences.
Javik says soon after that he read Shepard's physiology and nervous system, but considering the amount of Cerberus soldiers that had died in the area, it's not a stretch to say he's read that information from the blood on the ground, or from all the humans that had likely worked within the area. And again, Javik hadn't touched Shepard, so how could he have gotten that data from him?
HOW:
The cipher Shepard received from Shiala included the "biological instincts" of a Prothean. Perhaps through that cipher, Shepard's nervous system was trying to send and receive data it wasn't capable of. When Shepard died and was reconstructed through Cerberus, it could be that her some of her biology was rewritten to allow certain aspects of Prothean biology. For example, being able to see, to some degree, cloaked objects (i.e. Phantoms and Geth Hunters). This could be due to Cerberus regrowing biological tissue that fit Prothean patterns, or the implied "cybernetic enhancements" that Shepard received; perhaps nanobots that interacted with Shepard's nervous system. The latter is more likely, as it'd explain why it took some time for the ability to show itself.
Perhaps the reason that Shepard only demonstrated this ability with Javik, and never anywhere else, is because her mind was on the Protheans at the time and had been making good use of the cipher.
Tl;dr - Shepard touched Javik's armor and had a flashback to Javik's last moments, while Javik did not touch Shepard at all. The cipher is likely the cause for this ability.
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