Once she had obtained coordinates from John, the rest of it was relatively easy. The shuttle's computer still functioned properly and understood as to where she specifically wanted to go. After that, well, Jenny just had to sit back, pilot, and enjoy.

Overall: it made for one very long and boring trip to the Pegasus galaxy.

So, by the time she actually reached Atlantis, she was more than eager to get out of her ship and on to actual land and meet John and find out what happened to Rodney. As she flew in closer, she opened radio frequency.

"Hello? John? John Sheppard, are you about?"