The screen says there is no operating system

A laptop has two partitions in its hard drive and I was trying to fix it. The first part is totally shot, while the other one still have a 9Gb of free space. I used it as a place of recovery files, but I have to delete the recovery agent to leave a space for reinstallment.
I did this as a help for a college student who could not afford to buy a new computer. Now when I start up the computer, the screen says there is no operating system. I do have Windows Vista OEM, however, I could not get into the command prompt to run the setup. Please give me some advice. Thanks!
