[7] Esa Mäkelä, the captain of Silja Europa who was appointed on-scene commander for the subsequent rescue effort, described the weather as "normally bad", or like a typical autumn storm in the Baltic Sea.

The first sign of trouble aboard Estonia was when a metallic bang was heard, presumably caused by a heavy wave hitting the bow doors around 01:00, when the ship was on the outskirts of the Turku archipelago, but an inspection—limited to checking the indicator lights for the ramp and visor—showed no problems.

The radio operator on Silja Europa, chief mate Teijo Seppelin, replied in English: "Estonia, are you calling mayday?"

[1] MRCC Turku failed to acknowledge the Mayday immediately and Mariella's report was relayed by Helsinki Radio as the less urgent pan-pan message.

The former took survivors to shore, while the latter—Finnish border guard helicopters Super Puma OH-HVG and Agusta Bell 412 OH-HVD—chose the riskier option of landing on the ferries.

[1] Ships rescued 34 and helicopters 104; the ferries played a much smaller part than the planners had intended because it was too dangerous to launch their man-overboard (MOB) boats or lifeboats.

[12] The wreck was examined and videotaped by remotely operated underwater vehicles and by divers from a Norwegian company, Rockwater A/S, contracted for the investigation work.

[JAIC 4] The bow visor and ramp had been torn off at points that would not trigger an "open" or "unlatched" warning on the bridge, as is the case in normal operation or failure of the latches.

The report was critical of the crew's actions, particularly for failing to reduce speed before investigating the noises emanating from the bow, and for being unaware that the list was being caused by water entering the vehicle deck.

[JAIC 7] In 1999, special training requirements in crowd and crisis management and human behaviour were extended to crew on all passenger ships, and amendments were made to watch-keeping standards.

[14] New International Maritime Organization (IMO) Safety of Life at Sea (SOLAS) liferaft regulations for rescue from listing ships in rough water were introduced.

[15] New designs, the "citadel concept" once again influenced by Estonia, aim to ensure damaged ships have sufficient buoyancy to remain afloat, though cost will determine if any are built.

SOLAS 90, which came into effect in 2010, specifies existing passenger ships' stability requirements and those in North West Europe must also be able to survive 50 cm (20 in) of water on the car deck.

[17] The head of the Estonian investigation, Margus Kurm, stated publicly that he believes this new information points to a collision with a submarine and that the hole could not have happened post-sinking.

[19] The Swedish documentary makers were prosecuted for violating the sanctity of the wreck, but were acquitted on 8 February 2021 as the diving happened on a German ship in international waters.

[22] Shortly after, the Swedish Accident Investigation Authority announced their plan to conduct dives at the grave site starting in July 2021.

[24] Between 2021 and 2022, Estonian, Finnish and Swedish authorities carried out comprehensive wreck surveys[25] using cameras, 3D photogrammetry, 3D laser scanners, and shallow- and mid-penetration sub-bottom profilers, among other equipment.

German journalist Jutta Rabe and the British magazine New Statesman claim that laboratory tests on debris recovered illegally from Estonia's bow yielded trace evidence of a deliberate explosion, which they allege was concealed by the Swedish, British, and Russian governments to cover up an intelligence operation smuggling military hardware via the civilian ferry.

[32] Members of the Joint Accident Investigation Commission denied these claims, saying that the damage seen on the debris occurred during the visor's detachment from the vessel.

The JAIC cited results from Germany's Federal Institute for Materials Research and Testing, which found that Jutta Rabe's samples did not prove an explosion occurred.

[33] In the autumn of 2004, a former Swedish customs officer claimed on Sveriges Television that Estonia had been used to transport former Soviet military equipment in September 1994.

[34] The Swedish and Estonian governments subsequently launched separate investigations, which both confirmed that non-explosive military equipment was aboard the ship on 14 and 20 September 1994.