Looking for the name of a book series I read in middle school, 2001-2004 roughly. All I can remember about it was that there were a handful of teenagers who somehow ended up on an alien planet that they eventually found out to be a ship. They have to fight for survival against multiple different enemies, I think one of the kids could communicate with part of the ship telepathically. Some of the aliens were either blue or I think even transparent. There really isn't too much to work off of, but I figured someone might know what it is.
Since I don't think Katie is coming back, she realized (and posted in her question) that the series was Remnants by K.A. Applegate.
From the Wikipedia summary of the series:
It is the story of what happens to the survivors of a desperate mission to save a handful of human beings after an asteroid collides with the Earth. Eighty people are placed aboard a converted space shuttle using untested "quack" hibernation technology and fired blindly into space hours before all life on Earth is obliterated by a large asteroid called The Rock. They are then picked up by a large, sentient space craft of monumental proportions known as 'Mother' which is inhabited by various races. 'Mother' can manipulate the physical environment within the craft's limits and often does so. Only a few people placed in stasis actually were alive and capable of being reanimated when they reached 'Mother'.