The reason I asked about food, bedding, etc. is because if the answer was something like, "We found her dangling by her back foot from the wire mesh around the Tupperware box," or, "We gave her a lovely piece of raw sweet potato as a treat," then those things have some bearing on what may have happened. (For newer folks who may be reading this: raw sweet potato is a huge no-no. It turns into cyanide in a rat's stomach.) If she ate something that's bad for rats, it could have been the culprit. More info is often helpful in situations like this.
As jorats said, a small cage, seed mix, and lack of company aren't fatal, but they're not exactly good.