Caroline Davies and Tom Parfitt for The Guardian report:

The Arctic Sea was discovered 300 miles off the Cape Verde islands three weeks after it went missing, triggering speculation of a pirate attack.

Three weeks after it vanished at sea, the cargo ship Arctic Sea was found off the Cape Verde islands today with its Russian crew alive, well and “answering questions”.

All 15 sailors were aboard a Russian anti-submarine warship , bringing to a conclusion one of the most intriguing maritime mysteries of modern times.

But, even as the Russian authorities announced the development, the few details to emerge left more questions than answers at the end of a saga which has inspired frenzied rumours of piracy, ransom demands, secret cargoes and arms smuggling – all worthy of a cold war thriller.

Russia’s defence minister, Anatoly Serdyukov, informed the Russian president, Dmitry Medvedev, that the crew, when found, were not under armed control, and were now helping to “clarify” the circumstances of this most unusual incident.

Tass news agency quoted Serdyukov saying: “The Arctic Sea was discovered at 1am Moscow time today 300 miles off the Cape Verde islands.

“The crew have been moved to our anti-submarine warfare ship. They are answering questions … to clarify all circumstances of the incident. All crew members are alive and they are feeling well. They were not under armed control.”

Viktor Matveyev, the director of the Finnish-owned vessel’s operating company, Solchart, told the Komsomolskaya Pravda newspaper: “We are extremely pleased, we’ve been told everyone is alive and nobody was hurt … I can’t say any more. I’m rushing to a meeting to organise getting the crew home, checking their health and providing any help. We still don’t know what condition the ship is in”.

The disappearance of the Arctic Sea, carrying a £1.1m cargo of timber, baffled experts as it eluded radars and satellites and vanished after passing through the English Channel on July 28. Just how a 4,000 tonne ship could drop off the charts in these days of space-age technology prompted allusions to the Bermuda triangle and the “ghost ship” Marie Celeste.

Further intrigue came with reports that the Malta Maritime Authority had received information that the Maltese-registered vessel had been boarded by up to a dozen armed men in masks as it sailed through the Baltic Sea, sparking concerns of piracy – almost unheard of in European waters.

The “raiders” reportedly bound, blindfolded and beat the crew before departing in an inflatable boat 12 hours later, it was said, leaving the ship’s communications equipment damaged. The Arctic Sea had left Finland, bound for the Algerian port of Bejaia, on 23 July. It was known to have made contact with Dover coastguards on 28 July, but, at that point there had been no alert over the “attack” so there was no hunt for the ship.

Two days later it was spotted in the Bay of Biscay. Its automatic tracking system recorded its position at 1.30am. From then on, however, there was no further contact. The tracking system appeared either to have been switched off or to have stopped working from that day. It was due to make port in Algeria on 4 August. It now appears it changed direction, heading out into the western Atlantic.

The Kremlin had ordered warships and submarines to scour the Atlantic amid fears that the ship might have been the target of a second attack. Meanwhile, Nato was monitoring the situation, due to the unusual nature and location of the attacks, but was not directly involved .

Puzzling over speculation that the ship had fallen victim to pirates, a spokesman for the European commission, Martin Selmayr, said on Friday: “From information currently available it would seem that these acts, such as they have been reported, have nothing in common with ‘traditional’ acts of piracy or armed robbery at sea.”

Then, French officials reported the same day that a ship “resembling” the Arctic Sea had been spotted off the Cape Verde islands, west of Senegal, though there was no immediate confirmation of this.

The plot took a further twist at the weekend with unsubstantiated reports that the ship’s Finnish owners, who have denied its cargo is anything other than timber, had received a ransom note for a “large sum”, reported to be almost £1m.

But there was never confirmation whether this was genuine.

Since it went missing, unsubstantiated suggestions have been made that the ship might have been hijacked because it was carrying a “secret” shipment, such as drugs or arms, unknown to its crew or owners.

Russia’s Nato ambassador, Dmitry Rogozin, gave no indication of how, or by whom, the ship had been seized, and how the Russian military had managed to get the crew aboard the Russian-guided missile frigate Ladny.

He told Interfax: “We can say now that the operation has been carried through successfully. It was done with brilliance.”

So what happened?

Piracy: Was the ship attacked in the Baltic Sea?

Swedish police said the crew allegedly told their shipping company that up to 12 masked men, claiming to be Swedish anti-drugs police had boarded the vessel on July 24, one day after leaving Finland, tying up the crew before leaving in an inflatable boat after 12 hours.

Cargo: Was it carrying anything other than timber?

Not according to its owners. However, Mikhail Voitenko, editor of Russia’s Sovfracht maritime bulletin, fuelled intense speculation by suggesting on the Russia Today news channel that its cargo might not be drugs or arms, “but something much more expensive and dangerous”. He did not elaborate. “It seems some third party didn’t want this transit to be fulfilled so they made this situation highly sophisticated and very complicated,” he said. The operating company pointed out that the ship was checked by customs agents on leaving Kaliningrad, and in Finland. The Finnish Radiation and Nuclear Safety Authority dismissed as “stupid” claims of a nuclear cargo. Officials did conduct radiation tests on the ship at a port in Finland, but the head of the authority said there was “no basis’ for reports that a fireman had thought there might be some radioactivity involved.

Dispute: Were the Russian mafia involved?

The possibility that the Arctic Sea was involved in a commercial dispute, perhaps involving the Russian mafia, was widely rumoured. David Osler, who writes on Maritime Safety for Lloyd’s List, told the BBC’s Today programme: “It doesn’t look like it’s the sort of theft of a high-value ship or cargo. It looks like some sort of dispute between Russian interests”.