The purpose of MERS was to help in the securitization process. Basically, MERS directed defaulting mortgages to the appropriate tranches of mortgage bonds. MERS was essentially the operating table where the digitized mortgage notes were sliced and diced and rearranged so as to create the Mortgage Backed Securities. Think of MERS as Dr. Frankenstein’s operating table, where the beast got put together.
However, legally—and this is the important part—MERS didn’t hold any mortgage note: The true owner of the mortgage notes should have been the REMIC’s.
Every mortgage is recorded at the county. If a bank would merge, change it's name, sell the mortgages - the counties demanded that the mortage be re-recorded / modified to reflect the new bank name. This meant
a lot of $ for the counties
In comes MERS. Through contracts with their client banks, MERS would record the mortages in it's name. Then when the banks merged, sold the mortgages, etc, nothing need to change (at the county). Thus the banks avoided pay the counties for re-recording.
Looks like this has come back to bite them in the ass!