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Questions continue to swirl around a shipment of Iranian missiles the Israeli navy intercepted near Sudan, with experts saying the weapons' true destination might reveal a hidden agenda in Tehran.

A tricky trail of paperwork and the circuitous route of the Panama-flagged ship found to be carrying lethal M-302 missiles from Iran showed a major effort to hide the cargo and the parties involved. The Israeli Defense Forces say the weapons aboard the ship, now being towed to the southern Israeli port of Eilat on the Red Sea, were bound for the terrorist enclave of Gaza via the Sinai Peninsula.

“We are absolutely certain they [the missiles] were headed to Gaza,” Israel Defense Forces spokesman Peter Lerner told FoxNews.com. “The intelligence on this mission has been gathered over months. We know that it was supposed to probably go by land from Port Sudan via the Sinai Peninsula and into Gaza."

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While Iran has recently rebuilt close ties to Hamas operatives in Gaza, enhanced cooperation between Egypt and Israel has made smuggling goods from Sinai into Gaza difficult at best. The daunting logistics of such a smuggling operation, and the risks of confiscation of such valuable weapons, has given rise to speculation that the missiles were not meant to go beyond the Sinai. The lawless peninsula between Egypt's mainland and Israel has in recent years become a hotbed of jihadist activity.

“The obvious conclusion...is that a large part of the rockets on the arms ship – perhaps even all of them – were meant to reach Sinai and be activated from there,” suggested veteran award-winning Israeli war correspondent Ron Ben-Yishai in today’s ynetnews.com. “It's possible that the Gazans, (Hamas, the Islamic Jihad and the Popular Resistance Committees), were supposed to leave [Gaza] for Sinai, and build a hidden launching system there in an isolated area which the Egyptian army finds it difficult to reach and control.”

Since taking interim power in Egypt in 2013 Gen. Abdel Fattah el-Sisi has clamped down hard on terrorist groups in Sinai. There have been a series of fierce and bloody battles that have seen heavy losses on both sides, his forces have reportedly blown up the majority of the smuggling tunnels between Sinai and Hamas in Gaza and heavily patrol the once porous border, and the Egyptian courts moved only last week to declare Hamas a terrorist organization and closed down their offices on Egyptian soil.

Such a theory would suggest Iran is working at least to some degree with Al Qaeda, the terror network that has a strong grip in Sinai but which is currently fighting against Iran and President Bashar al-Assad in the Syrian War. Iran has long been at odds with Al Qaeda, but last month the U.S. Treasury Department accused Iranian-based operatives of working with and funding Al Qaeda linked groups fighting Assad in Syria. Analysts say it is likely that Iran is playing both sides in Syria's civil war.

“The moment that the [Syrian] regime collapses” Dr. Majid Rafizadeh, an Iranian-American political scientist and scholar at Harvard University, wrote on Al Arabiya last month, “Iran is likely to shift its political position and support any group that seems to come to power. From Iranian perspectives, the most powerful groups among the oppositions in Syria are currently the al-Qaeda linked groups. As a result, having close ties with al-Qaeda is paramount for Iran in case Assad is overthrown. For now, keeping a relationship and supporting both al-Qaeda and Assad is political opportunism for Tehran.

Had they reached their intended destination, whether in the Sinai or Gaza, the M-302 missiles may have been capable of exposing a current gap in Israel’s Iron Dome missile defense system that won’t be fully operational filled until 2016. Until then, such weapons could easily strike major population centers such as Tel Aviv, Jerusalem, and Haifa, causing potentially heavy casualties.

The cargo vessel named Klos C, owned by a Marshall Islands shipping company, was boarded by Israeli commandos off the coast of Eritrea coast and found to be carrying a load of Syrian-made M-302 missiles on board. Logistics of the shipment, which is believed to have originated in Syria and been transported through Iraq and Iran before beginning its sea journey from the Iranian port of Bandar Abbas, were complicated to avoid detection, according to reports. It is believed the shipment was to be unloaded in Sudan and then transferred by land to its final destination.

U.S. officials said the Pentagon was aware of the Israeli interdiction from the early stages, and Defense Secretary Chuck Hagel "reiterated the United States' commitment to holding Iran accountable for its destabilizing activities in the region, even as we continue efforts to resolve our concerns over Iran's nuclear program through diplomacy," Pentagon spokesman Navy Rear Adm. John Kirby said.

Ron Ben-Yishai suggests the missile consignment may have been intended to respond to a pre-emptive strike on Iran, should the current negotiations between the so-called P5+1 nations fail to produce a nuclear draw-down in Iran.

“The Quds Force [Iranian Revolutionary Guard] organized a very complicated logistic operation here, which cost tens of millions of dollars and was carried out secretly while risking an exposure of the violation of UN sanctions by Iran and the Syrian regime. It's reasonable to assume that this is a response scenario to an IDF and/or American attack on Iran's nuclear facilities.”

Although re-iterating Israel’s firm belief that the weapons hidden on the intercepted ship were headed directly to Gaza, Lerner conceded that, “Iran will dabble in anything that serves its interests of arming, training, and funding terrorist organizations. It would not be beyond reasonable that they would facilitate Al Qaeda factions in Sinai. They operate with these types of people in Yemen and other places around the world.”

Paul Alster is an Israel-based journalist who can be followed on twitter @ paul_alster and at www.paulalster.com