G.I. Joe: The Complete Collection #2

After the bunker was bombed by Baroness and Scar-Face,sinking it underwater (trapping Snake-Eyes, Kwinn, and Dr. Venom inside), Stalker, Breaker, Gung-Ho call the Joes for pickup from Rio Lindo while the country's under hostile takeover (thinking the three inside dead). The three Joes recover a briefcase left on purpose by the Commander as a ruse to trick the Joes while he continues with his real plan, and are rescued and take the false plans back to headquarters none the wiser of the real plan. The story ends with a familiar Morse Code tap coming from the bunker.