Since you already are able to boot to a command line, you may try to repair the damage done by the crash to the OS2.ini file.Cd to the C:\OS2 directory and check for the existence of the following files: OS2.INI and INI.RC. Note that OS2.INI may be a hidden file, thus use DIR /A to ascertain its presence.
Assuming that you are already in the C:\OS2 directory, type the following command exactly:
MAKEINI OS2.INI INI.RC
It will reinitialize all Workplace Shell objects and possibly will make you happy by the shell reapearing after a reboot.
If that does not work then your only other option is to recover from an archive that you may have already done from the Settings Notebook before the crash. Upon an initial boot OS/2 displays a small white square at the upper left corner of your screen. BEFORE the square disappears, press SIMULTANEOUSLY and hold the Alt and F1 buttons on your keyboard. You will be presented with several options including the original archive (done automatically by OS/2 when it was first installed) and any other archives that may have been done by you or anybody before you.
Note that you will loose any icons that you had if you choose a relatively aged archive-- such as the one done originally by OS/2. The installed applications continue there, however, and can be started from the command line.
If you decide to reformat the OS/2 partition, the most straightforward manner is to download the compressed file IDEDASD.EXE from IBM and update diskette 1 with the drivers contained in the compressed file. Follow the instructions provided once you expand the file of reference.
If you need an overview on how to update diskette 1, check out the following:
http://www.computing.net/os2/wwwboard/forum/1829.html