Environmentalist group Sea Shepherd had been tailing the Thunder -- subject of an Interpol "purple notice" for suspected fraud and fisheries-related crimes -- since its ship the Bob Barker encountered it in the Southern Ocean several months ago.
The pursuit ended early Monday in the Gulf of Guinea, off the coast of west Africa, when the Bob Barker received a distress call from the Thunder.
"We were literally a few hundred meters away; they said the ship was sinking and they were abandoning the Thunder," said Sea Shepherd spokesman Adam Burling.
"We invited the crew -- 40 of them -- on board, had a medical officer check them over, provided them with food and water."
Bob Barker Captain Peter Hammarstedt said the crew rescued from the ship had been handed over to the Sao Tome coastguard early Tuesday.
He said he hoped the authorities would work with Interpol to prosecute those operating the vessel.
"We obviously want to see the captain of the Thunder prosecuted for his offenses," he told CNN by phone from the Bob Barker, at sea to the west of Sao Tome.
Hammarstedt said he believed the Thunder was deliberately sunk to destroy physical evidence of illegal fishing.
"I'm 100% confident that the captain of the Thunder destroyed his own ship," he said.
Hammarstedt said he had managed to send three crew members aboard the abandoned Thunder before it went down.
"Usually what happens when a vessel is sinking is the master will ensure all compartments and hatches are shut so as to maintain buoyancy," he said.
"On the Thunder, all the hatches had been opened, including the hatch leading to the fish hold."
Possible evidence recovered
He said his crew had retrieved computers, mobile phones and other devices from the Thunder that would be handed over to assist any investigation.
They had also retrieved a fish from the ship's fish hold, which he said was about a quarter full.
He said the fish was a toothfish, the prized stock his organization claims the Thunder was illegally catching when they were encountered in the Southern Ocean.
More surprising was the reaction of the captain of the Thunder as his ship went under, he claimed.
"When the vessel went completely under the water, the captain of the Thunder, who was in a life raft at the time, started cheering and applauding, which was very unusual behavior for a skipper who had just lost his ship," he said.
The pursuit of the Thunder began after the Bob Barker encountered the vessel off the coast of Antarctica, said Burling.
He claimed the vessel was found with its nets in the water, illegally catching Patagonian toothfish.
The Thunder dropped its nets and left the scene; a second Sea Shepherd vessel that was brought in to retrieve the net found about $3 million of toothfish catch in about 72km of illegal gillnet, he claimed.
"That's why they're out there in these shadowlands, these unpatrolled remote regions," he said.
Meanwhile the Bob Barker, supported by a second Sea Shepherd vessel, pursued the Thunder all the way to the Gulf of Guinea.
During that time, Burling claimed, the Bob Barker narrowly avoided being rammed by the fishing vessel, while its smaller boats were struck with grappling hooks.
The rescue had gone smoothly despite the months of tensions between the two vessels, said Burling.
"We worried what they might be like to our crew, whether they might be hostile or violent to us," he said.
But the Indonesian crew who made up the majority of those on board the Thunder seemed "very relieved" to be rescued.
The officers -- who he believed were Spanish -- were less so.
"Perhaps they would have preferred to have been rescued by someone else, but given the location there was really no other option," he said.
An Interpol "purple notice,"
released at the request of New Zealand in December 2013, put out a global call for information on the Thunder, as well as information on "the individuals and networks that own, operate and profit from the illegal actions of the vessel."
It said the vessel had changed its name, national registration and other characteristics a number of times to avoid detection of its illegal fishing activities, and had sailed under the names "Wuhan N 4" and "Kuko," and under the flags of Nigeria and Mongolia.
The Interpol notice said it had "conflicting information" about the identity of the vessel's current operator, but said it had previously been registered as owned by companies in Spain, the Seychelles and Nigeria.
Interpol confirmed Tuesday that the purple notice remained in place. It said it had monitored the situation and noted that all the vessel's crew members were safely ashore.
"Interpol does not conduct investigations itself; however, we remain available to support any national law enforcement authorities with jurisdiction in this case if such assistance is requested," it told CNN.
It said no requests had been received as yet.