We have no idea how far "our" people have made it into the Traveler. It is a rather massive structure so it is possible that not everything has been explored. We may have only gained access to less sensitive areas with more "dangerous" command and control, life sustaining or secure cargo/armories/magazines being locked. Once again if the technology is sufficiently far beyond us then how would we gain access? Also keep in mind that sentient doesn't have to refer to a biological life form, especially as we know or can imagine them. The simplest answer that is easily conceivable is that the Traveler is an A.I. construct tucked away inside this vast space fairing vessel. Maybe it was damaged to the point of being in what amounts to a coma for a biological being. If that is the case its "body" is just sitting there waiting for a command from the mind but none has come. It is also very possible that there were other biological beings on board but they were killed in the battle leaving their ship to just sit idle. While we bumble our way about trying to figure out how to turn the lights on we may not yet know the price that was paid by the crew. For that matter all this time we have believed that the Traveler saved us when maybe all that really happened was that the species that built the Traveler were fighting a war that they were already involved in. The crew of this particular ship never made it home but inadvertently managed to save our entire species. Another could be as simple as the fairly small crew left on this ship put themselves in stasis. They found their ship badly damaged, incapable of long duration voyages while the planet that they have come to rest near has an atmosphere too toxic for their kind. They sent out a distress call to their home star, locked the ships functions down and settled in for a long cold sleep until help could arrive. Little did they know, that call never made it home and their slumber has lasted for three centuries. Alternatively to that last one, you could say that they knew it would take this long for help to come. They will wake up at some point in the near future when the recovery ship gets closer. Either of these could also lead to a new playable race. You see, with just a little bit of thought you can make any number of things happen. We are currently starting from a fairly blank slate so there are few limits. Just take any plausible explanation and flesh it out until you have a story. I have always found a good writing tip to be: "Ask yourself why a lot". The reason for this is simple, it forces you to figure out how these people got to where they are, what makes things work they way they do. Few questions are as useful as "why". It also has the added benefit of showing you which things simply don't make sense. As you said, they may simply be in hiding. Now we could ask "why" and give that a whole story all its own, but I will leave that to you. It was your idea after all.