The job of the MM is to provide market liquidity. They match the buyer and the seller. But, if an order comes in with no matching order in que, the MM steps in and uses shares out of it's own inventory to complete the transaction. That way trade orders aren't sitting there waiting for a match. If the MM does use shares out of their own inventory, they are not getting their cut (bid/ask spread). So what they do is short the stock and cover it with shares out of their own inventory, if they have enough shares in inventory. If they don't have enough to cover, say hello to "naked shorting".
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