Undated photo of the Maltese-registered, Finnish-chartered vessel, Arctic Sea, that mysteriously disappeared off the coast of France two weeks agoReuters – Undated photo of the Maltese-registered, Finnish-chartered vessel, Arctic Sea. REUTERS/SOVFRACHT

In July, the Russian-manned cargo ship the Arctic Sea disappeared on its way to take timber from Finland to Algeria, sparking reports of the first incident of piracy in European waters since the days of the buccaneers. Experts and observers weighed in with their theories: the ship had been snatched in a commercial dispute; it was being used to run drugs; it was carrying something more precious - or dangerous - than timber.

Since then, the Russian navy has found the ship, and the alleged hijackers who boarded it on July 24 have been charged with kidnapping and piracy. The ship's captain, his crew and whatever cargo the ship was carrying have also been detained. An initial search of the hull turned up nothing suspicious, and now Russia's official explanation of what happened will probably become the final one - this was a hijacking thwarted by its navy without a shot being fired. But there are baffling details left unexplained, leading some experts to claim that the truth is much more sinister: the Arctic Sea, they say, was intercepted by Israel as it carried a secret cargo of weapons to the Middle East.(See pictures of dramatic pirate-hostage rescues.)

The highest-ranking official to put forward this version of events is the European Union's rapporteur on piracy and a former commander of the Estonian armed forces, Admiral Tarmo Kouts. In an interview with TIME, he says only a shipment of missiles could account for Russia's bizarre behavior throughout the monthlong saga. "There is the idea that there were missiles aboard, and one can't explain this situation in any other way," he says. "As a sailor with years of experience, I can tell you that the official versions are not realistic."

Kouts says an Israeli interception of the cargo is the most likely explanation. But this theory, which some Russian analysts put forward in the days after the Arctic Sea was rescued and which Kouts agreed with in his interview with TIME, has been vehemently denied by Russia's envoy to NATO, Dmitri Rogozin, who says Kouts should stop "running his mouth." (Read "Girding for the Pirates' Revenge.")

The official explanation coming out of Moscow is simple enough: the Arctic Sea, manned by a Russian crew, set sail from Finland under a Maltese flag on July 22. It was destined for Algeria and carried less than $2 million worth of timber. Then a group of eight Russian and former Soviet hijackers boarded the ship on July 24. The ship's tracking device was disabled in the last days of July, as it passed through the English Channel into the Atlantic, and the ship disappeared. On Aug. 12, the Russian navy sent out a search party. A week later, Russia declared that the ship and its crew had been rescued. (Read "Has Piracy Spread to Europe's Waters?")

But as details of the hijacking emerged, the tale got murkier, and Moscow's explanation does little to clear things up. Why, with so many other ships carrying much more valuable cargo, would the hijackers target theArctic Sea and its small load of timber? Why didn't the ship send out a distress signal? Why did Israeli President Shimon Peres pay a surprise visit to Russia a day after the ship was rescued? Why did Russia wait so long to send its navy to find the ship? And what did the brother of one of the alleged hijackers, Dmitri Bartenev, mean when he told Estonian TV on Aug. 24 that his brother and the other suspected pirates had been "set up ... They went to find work and ended up in a political conflict. Now they are hostage to some kind of political game"? Bartenev's lawyer tells TIME that his client was "in the wrong place at the wrong time."

There are also questions surrounding the Arctic Sea's rescue. On orders from the Kremlin, Defense Minister Anatoly Serdyukov sent a completely disproportionate force, including destroyers and submarines, to look for the vessel. It took five days for them to find it, the Defense Ministry said, even though the Foreign Ministry later announced that it was fully aware of the Arctic Sea's coordinates the entire time. To fly the alleged pirates and the crew back to Moscow - a group of only 19 men - Russia dispatched two enormous military-cargo planes. And then on their arrival, the ship's crew was detained along with the alleged hijackers for days of questioning, with no access to their families or the media.

"Even from the basic facts, without assumptions, it is clear that this was not just piracy," says Mikhail Voitenko, editor of the Russian maritime journal Sovfrakht, which has been tracking unusual incidents on the high seas for decades. "I've never seen anything like this. These are some of the most heavily policed waters in the world. You cannot just hide a ship there for weeks without government involvement."

Read "Russia's Moves Raise Doubts About Obama's 'Reset.' "

See pictures of Somali pirates.

According to Voitenko and other experts, a secret cargo could have been hidden on the ship during the two weeks it spent in Kaliningrad for repairs, just before it picked up its Finnish haul of timber. Not contiguous with the rest of Russia, Kaliningrad is the country's westernmost enclave on the coast of the Baltic Sea, and is known as a hub for Russian smugglers. "Personally, I don't care about any missiles," Voitenko tells TIME. "I care about what they're doing with those sailors."

There are many governments, however, that would be more concerned about a possible missile shipment, especially if it were destined for the Middle East. Chief among them is Israel. In recent years, the Israeli government has consistently raised alarms about Russia's plans to sell MiG-31 fighter planes to Syria and its construction of a nuclear-power station in southwestern Iran. Negotiations with Moscow have been tough on these issues and relations often icy, as the Israeli President pointed out during his visit to Russia on Aug. 18, just as the mysteries behind the Arctic Sea's disappearance began to unfold. (Read "Medvedev and Obama: Sunshine in Moscow.")

"The most likely explanation is that the Israelis intercepted this cargo, which had been meant for Syria orIran," says Yulya Latynina, a prominent political commentator and radio host on Echo of Moscow, a station owned by state-controlled gas giant Gazprom. "They will now use the incident as a bargaining chip with Russia over weapons sales in the region, while allowing Russia to save face by taking its empty ship back home." When contacted by TIME, both the Israeli Prime Minister's office and Mossad, Israel's secret service, declined to comment. (See pictures of 60 years of Israel.)

But in an Aug. 18 statement, the Israeli Foreign Ministry said that Peres had discussed "the sale of Russian weapons and military hardware to countries hostile to Israel" with his Russian counterpart, Dmitri Medvedev, on that day during four hours of closed-door talks in the Russian city of Sochi. According to the statement, Peres "stressed that Israel has concrete proof of Russian weapons being transferred to terrorist organizations by Iran and Syria, especially to Hamas and Hizballah." A spokeswoman for the Israeli President declined to elaborate on any connection with the Arctic Sea. In a parallel statement, the Kremlin did not mention weapons sales, saying after the meeting that "we more clearly and precisely understand each other's positions."

Russia's chief investigator, Alexander Bastrykin, told official state newspaper Rossiyskaya Gazeta that a band of new-age pirates, possibly in connivance with the crew, is all that lies behind the Arctic Sea mystery. But he did concede that there are questions that need answering. "We don't rule out the possibility that [the ship] was carrying more than just timber," he said, without elaborating further.

Speaking to TIME, NATO envoy Rogozin backed up the investigator's statement: "The cargo has to be checked to see if there was something illegal, something being smuggled." But he declined to comment on the theory of Israeli interception. "This is no longer a question for diplomats or for the military," he said. "It is now a question for the investigators, and they are carrying on with their work. We are also very curious to hear their findings." (See pictures of the face of modern piracy.)

When asked by TIME about the possibility that the Arctic Sea was carrying a secret cargo, Vladimir Voronov, deputy head of Oy Solchart Management - the Helsinki-based, Russian-run company that operates the ship - replied, "I don't know anything about a secret cargo. We're just a simple shipping firm, and from what we understand, our ship was hijacked."

According to investigator Bastrykin, a full search of the vessel will be carried out when the ship arrives at a Russian port in the next few weeks. But observers don't expect any revelations. "The versions we are getting from the Russian government do not fit into any logical parameters, and I don't think that will change," commentator Latynina says. "When people lie, they tend to lie consistently."