If the check was deposited by the company to its bank account, that bank made a warranty to you that it credited it to the account of the payee, but if the check was somehow diverted and deposited into a different account, you'll need the cooperation of the company to whom you made out the check out. Your bank should have a form for an affidavit that the payee of the check can sign and give back to you. Although apparently the payee's endorsement is missing, rather than forged, I believe that the more or less standard affidavit of forged endorsement should work.
When you receive that affidavit back from the payee, you can take it and the check to your bank and ask them to pursue a claim with the depository bank (which your bank can identify from the hieroglyphics on the back of the check). You should be able to recover your money that way. It's too late for your bank to return the check without the affidavit.
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