One of the few pieces of declassified evidence showing John McNaughton’s role in the Jupiter removal process, his report to McGeorge Bundy concerned the “physical operation” to remove the missiles and the related press management.  Dismantlement actions would begin on April 1 in Italy and April 15 in Turkey.  For both countries, the dismantled missiles would go to a “graveyard.” The arrival of Polaris submarines during April would be publicized along with a visit to Turkey around April 14-15. No photographers would be allowed on site, but no “special limitations” would apply when the missiles were in transit. One of McNaughton’s concerns was that the dismantling operation be handled in a way that “reduced[d] … erroneous comparisons with Cuba.”

Kennedy, McNamara and Rusk moved ahead with the Jupiters matter by making plans to bring it up with Italian and Turkish defense ministers at the NATO meeting in Paris in December 1962. The goal would be to persuade them of the obsolescence of the Jupiters, the dangers that they posed during the Cuban crisis and in future crises, and the need for “better arrangements,” such as “a rearrangement of Polaris deployments.”

President Kennedy continued to monitor the Jupiter missiles problem. During a meeting with Rusk a few weeks later, McNamara explained that President Kennedy, who he had seen in Palm Beach on December 27, had asked him what steps were being taken “to remove the Jupiters.” Consistent with that, McNamara favored the “earliest possible date” and asked whether a “deadline” could be set for April 1 to begin the removals.

Seymour Weiss would push back against any efforts to remove the Jupiters, but he and others realized that President Kennedy had a “keen interest” in the matter and that Secretary of Defense McNamara had ordered that action be taken (assigning his General Counsel John McNaughton to take the lead). Nevertheless Weiss and Assistant Secretary of State William Tyler presented Secretary of State Rusk with a memorandum making the case against action on the Jupiters or at least postponing their removal until a “later time.” Paralleling arguments made during the crisis by Ambassadors Hare and Reinhardt, Tyler pointed to the “symbolic and psychological importance” of the Jupiter deployments. While Tyler noted parenthetically that the Italians had “given indications of a disposition to work toward the eventual removal of the Jupiters,” the U.S. could not phase them out “without general Alliance agreement,” including Italy and Turkey’s consent, “unless we are prepared to lay ourselves open to the charge of abrogation of specific or implied agreements.” Rusk was in the know on the secret deal, but his reference to a “later time” was consistent with it and signing the memo would have placated Tyler and Weiss.