No there is no guarantee that Factory Recovery will always work. That's why you should make the Recovery disks to have another method in case running Recovery from its partition fails. If both methods fail then you can Clean Reinstall.
Had you posted your Specs or even mentioned the computer brand we could have provided the exact steps to recover.
But first there is a long list of steps to take to assure everything's been done to repair the OS in
Troubleshooting Steps for Windows 7 and
Troubleshooting Windows 7 Failure to Boot.
What were the results of the Malwarebytes scan? If it won't run then download, burn to CD and run a full scan with
Windows Defender Offline.
We need to see how serious the infection is. It may require advanced removal tools such as
Combofix to repair infection.