I have to ask this first: What OS are we dealing with?
Can there be a BIOS infection: Yes.
Will it affect your system like this: probably not, but not completely out of the question
The BIOS is a small chip and (not to take away from EvanDavis) it has been a VERY long time since I have seen a hardware virus. A BIOS virus would have to be accompanied by a software infection in the system. A BIOS infection would not automatically download software, as a BIOS configuration is only at the basic hardware level, hence the name Basic Input Output System.
If you are concerned about the BIOS being infected, you need to get to the website of the manufacturer of the system board in your machine first. Download the latest BIOS update for the system. Depending on how your system is configured, you may have to work with the update to get it installed. Typically, the installation is done via floppy disc. Some can be updated from bootable CD, but that is something that will be outlined on the website for the update. Some of the newer updates are coming as software that runs on your machine, in Windows, and loads information to the boot record of the hard drive so that the software can be run and loaded into the CMOS chip. This option is not a viable one if you suspect a BIOS infection, as the software in the OS will hijack the function and probably cause you to have to re-flash the BIOS. Worst case scenario, the software hijacks the flash program and causes it to only work part of the way and when you reboot, dead machine requiring a replacement of the CMOS chip (which is most likely soldered on) or replacement of the board (due to the aforementioned solder).
If you have an infection of the OS that is this deep, I recommend that you obtain the toolkit from the manufacturer of your hard drive. This will allow you to boot to a CD (most likely) and perform a low level format on the drive. This will write zeroes to the drive and essentially "reset" it to a like new configuration. The idea is that the drive is written and re-written with zeroes to remove any instance of unwanted software. The process can take some time to perform but, in the end, you should end up with a clean drive on which you can install your OS.
Food for thought.