encrypt[plaintext_, polybius_, key_] := Module[{fraction, fractioned},
   fraction = Thread[Characters[polybius] -> Tuples[Characters["ADFGVX"], 2]];
   fractioned = Partition[Flatten[Characters[plaintext] /. fraction], UpTo[StringLength[key]]];
   StringJoin[Flatten[Part[Flatten[fractioned, {2}], Ordering[Characters[key]]]]]];

decrypt[encrypted_, polybius_, key_] := Module[{perm, colLengths, fractioned, defraction},
   perm = Ordering[Characters[key]];
   colLengths = Length /@ Part[Flatten[Partition[Characters[encrypted], UpTo[Length[perm]]], {2}], perm];
   fractioned = Flatten[Part[TakeList[Characters[encrypted], colLengths], InversePermutation[perm]], {2}];
   defraction = Thread[Tuples[Characters["ADFGVX"], 2] -> Characters[polybius]];
   StringJoin[Partition[Flatten[fractioned], 2] /. defraction]];

words = ReadList["unixdict.txt", Word];
key = Select[words, StringLength[#] == 9 && DuplicateFreeQ[Characters[#]] &] // RandomChoice;
polybius = StringJoin@RandomSample@Characters["ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"];
plaintext = "ATTACKAT1200AM";
encrypted = encrypt[plaintext, polybius, key];
decrypted = decrypt[encrypted, polybius, key];

Print["Key: ", key];
Print["Polybius: ", polybius];
Print["Plaintext: ", plaintext];
Print["Encrypted: ", encrypted];
Print["Decrypted: ", decrypted];