duplicate bridge rules for revoke,and any penatly should be imposed
The Short Answer: The Director finds which card is missing and restores the player's hand. This card is considered to have belonged continuously to the owner's hand, and as a result may have caused an accidental revoke, which is penalized as if it was any normal revoke.

The long answer:

The first step of a Director in this circumstance is to review each of the tricks, starting with the most recent, until a irregularity is detected. Most likely, the player with 3 cards left will eventually find a trick where they played 2 cards, at which point law 67: Defective Trick handles the rest:


  
  (a) When the offender has played more than
  one card to the defective trick, the Director
  inspects the played cards and requires the
  offender to restore to his hand all extra
  cards, leaving among the played cards the
  one faced in playing to the defective trick
  (if the Director is unable to determine which
  card was faced, the offender leaves the
  highest ranking of the cards that he could
  legally have played to the trick). Ownership
  of the defective trick does not change.
  
  (b) A restored card is deemed to have
  belonged continuously to the offender’s
  hand, and a failure to have played it to an
  earlier trick may constitute a revoke.
  
  
  The Director should avoid, when possible, exposing
  a defender’s played cards, but if an extra card to be
  restored to a defender’s hand has been exposed, it
  becomes a penalty card (see Law 50).


Should the rewind result in what appears to be normal play, then the card must be either on the ground/otherwise hidden, or it doesn't exist. Law 14 gives the solution for this problem:


  
  if the card is found elsewhere, it is restored
  to the deficient hand. Rectification and/or
  penalties may apply (see 4 following).
  if the card cannot be found, the deal
  is reconstructed using another pack.
  Rectification and/or penalties may apply
  (see 4 following).
  a card restored to a hand under the provisions
  of Section B of this Law is deemed to have
  belonged continuously to the deficient hand.
  It may become a penalty card, and failure to
  have played it may constitute a revoke.
  


The same concept is used if a card is missing during the auction/ just prior to the play: The hand is re-constructed by finding the card or using a new deck, and the hand continues as if the offender had the card all along. However, in any case, the fact that there was a missing card is unauthorized information should it happen after the first call, and Director should make sure that partner doesn't make any inferences based on the fact that some/all of the offender's calls or plays were made with 12 cards.

There's also the highly unlikely but amusing possibility that the problem isn't that one player is missing a card, but three players have an extra card. This results in a similar process, but a much harsher one, as a player who played no card to a trick would "complete" it by playing a card (following suit if possible,) but counting that play as an automatic revoke regardless. If it turns out they had an extra card before the play of the cards, then it's entirely up to a Director judgment call as to whether the situation can be rectified (usually no) or if adjusted scores are required.