Many of Shepard's actions carry across all three Mass Effect games, but one, in particular, connects to a squadmate in Mass Effect 3. It's subtle, and many didn't think too much of it besides simply being a side quest with some interesting lore about the relationship between humans and protheans. In general, the protheans have been a major part of the Mass Effect series, especially in the first Mass Effect game, but it was a nice surprise that Shepard eventually acquired a prothean squadmate later in the series.
Prothean ruins had a big effect on the universe, allowing species to find the mass relays, advancing technology and leaving behind plenty to study and wonder about. However, no one really understood the protheans until actually meeting on. When they did, an encounter from Mass Effect that many players may not have even seen was revealed to have a connection to Javik, the prothean squadmate.
In the first ME, there is a side mission on the Citadel to assist an asari consort, Sha'ira, who is having an issue with one of her clients. It's a fairly simple mission involving talking to a few people to straighten things out. However, instead of the typical rewards like items or credits, Shepard has the option to accept some advice and a mysterious pendant or refuse it for other favors. This pendant seemingly sits in Shepard's inventory for a while with no real information on how to use it, but diligent players may come across an item to use it with.
On the planet Eletania, there is a prothean artifact unlike the others encountered across the game. It's not marked differently from other anomalies on the map, so players will most likely just stumble across it. The artifact is a chrome-looking orb; upon inspecting it a second time, Shepard notices a hidden slot that the pendant can be placed in. This leads to some interesting text about the protheans watching over the first humans and studying them. The experiment or study is seemingly cut short as the device for watching them is removed, and the connection to Shepard severs, leaving them somewhat confused and unable to explain what happened. It seems like just a piece of lore that isn't mentioned in the second game; however, in ME3, this bit of trivia resurfaces with Javik.
After waking him up on Eden Prime and speaking with him on the Normandy, everyone has questions for him, especially Liara. However, if Shepard completed the side mission and obtained the artifact in ME1, then they will have the chance to ask Javik about the protheans studying humans based on this information. He will confirm that they were indeed studying and influencing other species and that humans were among them. Protheans would cultivate and uplift species they considered worthy of joining their empire. It was a great moment connecting both games.
Javik explains that this process stopped once the Reapers invaded because they wanted to protect the more primitive species from destruction. This was also reflected in the vision as the tracking technology is removed. However, it's unclear if the protheans removed it or the Reapers because they also remove traces of previous cycles. In the vision, the human hears a deafening sound before being pulled into a red beam which sounds very much like a Reaper.
As we learn more about the protheans, it turns out that they would all be brought into the prothean fold and live under its empire rather than being a galaxy of many different species. This apparently meant using similar technologies and folding all cultures into one as prothean architecture, devices and technology seem to follow a specific style. Humans and asari were meant to join them eventually, but it wasn't to be, luckily for them.
Most wouldn't have guessed this strange and long side mission from ME1 would be a huge insight into the protheans or that Javik would even mention this amount of detail in ME3. BioWare did a great job fleshing out the prothean empire and its lore through the ruins, and Javik's information and personality tied it all in perfectly. The prothean orb on Eletania turned out to be the greatest insight into true prothean culture -- even more so than Ilos.