This is a detailed guide to all dangerous animals in Endless Ocean 2, sorted by location. This includes some that only appear during certain missions.
In the main story, a sound from Oceana's pendant causes a Humpback Whale to turn violent and attempt to ram the player. After dodging it there, the whale remains calm through the rest of the game. Other than that, there are no other dangers.
In the main story, an aggressive Tiger Shark corners Oceana down in the Mouth of Truth, and must be pulsed. If you return after your first visit, it can be found swimming around the Coliseum, but only at night.
During the story mode, a Great White Shark attacks your party in the central area, but it is not there otherwise. After you discover the Triton Village Ruins, Thanatos will appear and attack. He is immune to the Pulsar, and must simply be avoided. Outside the main story, there are two groups of Great Whites patrolling the area, one up north, and one down south. The northern group patrols the Wreck of the Flamingo by day, and moves to the Wreck of the Pride of Athens at night, (while the Wreck of the Flamingo is patrolled by harmless Sand Tigers at that time). The group in the south patrols the Wreck of the Emerald Lady no matter what time of day it is, with Thanatos (after his encounter in the main plot) appearing alongside them at night. In the "Memento" mission, Thanatos appears yet again to attack your group. In another mission, you must dodge three Great Whites in the Red Dome, in order to grab a piece of the cave's carving. In the "White Dolphin of Cicero's" mission, a tiger shark is seen attacking the Albino Bottlenose Dolphin at Cross Rift.
The only dangers within the castle are Luna Lionfish, who are still dangerous despite their non-aggressiveness. There are small groups in two different rooms near the Underwater Gallery, along with a lone specimen hovering around the throne in Mermaid's Ballroom. Though Thanatos is seen swimming outside the windows, he cannot attack.
North Coast of Canada:
There are three Greenland Sharks patrolling the area. One is seen directly south of the ice hole inhabited by Narwhals. Another is seen near the Ice Mosaic, and another is seen lurking near the two ice holes in the northwestern area. The one near the Ice Mosaic is encountered in the plot. Here, the player is unable to turn back, as at this point in the story, they cannot stay in cold waters for too long. Though Jean-Eric asks the player to simply ride on their dolphin partner to get past him, he can optionally be pulsed before doing so. Though all of the sharks here are aggressive if approached too closely, they can be avoided if the player is riding on the Ancient Mother (provided that she is unlocked), or any other blue whale. While they will still attack the whale itself, neither it nor the player will take damage from it.
Though the area houses no dangers, a Great White is seen swimming around the bottom of the southwestern iceberg, but only during the "Ancient Ice" mission.
No dangers whatsoever, though in the main story, a Leopard Seal must be used to ram through some icicles blocking the path deeper into the cave. He must be dodged as he rams into the barricade, but he is non-threatening otherwise.
Cortica River Midstream:
In Perilous Waters, many swarms of Red Piranhas are present. They are easy to slip past, and will only attack if you swim too close to them. Further on, near the Eastern Sandbank and the Western Sandbank, many Spectacled Caimans are seen swimming nearby. The young ones are harmless, but some of the grown-ups will attack, with no visual indicator of exactly which ones will. Some can be seen on land, but these ones will not attack, and can be fed and pet. In the Mangrove Maze, Electric Eels are present, and due to their electric capabilities, they are immune to the Pulsar. They must either be dodged, or frightened off with the Sea Whistle.
Cortica River Upstream:
The area itself has no dangerous animals. However, there is a side-quest where you must take a photographer into the northwestern area to photograph sea turtles laying their eggs at night. On the way to that area, Great Whites are present to hinder you, and must be fended off with the Pulsar. The next part of this side-quest takes place during the day. Here, you must search for your partner's dropped camera equipment while avoiding the Tiger Sharks that appear alongside the Great Whites. Although Leviathan can be seen out to the far east of the map, he is completely harmless despite him being described as ferocious. It is also worth nothing that the sharks present in the aforementioned missions are not present ever again afterwards.
Zahhab Region Depths:
In the main story, a Giant Squid blocks off the entrance to the Secret Passage connecting the two crevasses. He does not physically attack in any way, but the player will not be able to pass him. Luring a Sperm Whale towards him makes the whale swim at full force, and must be dodged. After this, the squid and the whale can still be seen in the Twin Crevasses, either swimming separately or attacking each other, but they do not attack. (In fact, when the two are battling, they can still be approached, and clicking on them causes the name "Deep-Sea Battle" to show on the screen). In the far-east corner of the South Crevasse, a Bluntnose Sixgill Shark can be found lurking near the Twin Caves, (the shark and the area do not play a role in the main story), and after pulsing him, the caves can be explored freely until the effects of the Pulsar wear off.
Cavern of the Gods:
After exploring the ruins for a bit, your party will be blocked off from the Celestial Mausoleum by a door. While pondering over how to get through, a pair of Goblin Sharks attack the group. Pulsing them makes them swim away, and at that moment, GG opens the door. After a brief reading through the writing on the walls, the sharks return, this time along with the Okeanos's Guardian, and they must be pulsed. While the sharks are temporarily tranquilized, you must swim to one of the three altars around the room and insert one piece of the Dragon Flute. Each time you do this, the pulsar will wear off, forcing you to repeat the process twice more. Afterwards, the trio swims off, and are not seen again for the rest of the story. It is also worth noting that after all of the whales start to destroy the temple, the game will send you back to the starting point of the escape route if you swim too close to one of them.
After reopening the cavern, the same three sharks are seen patrolling the Pillars of Shadow, (with the Okeanos's Guardian hovering near the door at the top of the room), but only at night. It is best to do whatever you're doing quickly, and not let your guard down when the sharks are around, as all three of them shake off the Pulsar's effects very quickly (Though most of the secrets in this room can be found during the day).