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Yes there are. This game features an unique 3-way branching story with quite a few substantial differences in plot and puzzles between the storylines.

The first part of the story is scripted, and the player has little influence on general story outcome (you can perform actions at will, but there are sequences of actions that need to be taken to advance the scripted chain of events). The story is fixed up to the moment where Indy and Sophia return to Barnett College to find Plato's Lost Dialogue. There are three random locations where the book can be (this also has no effect on story outcome). After Indy has found the book, he returns to his office for a talk with Sophia. Sophia will then start to predict his future. This prediction summarizes the way you handled challenges in the game up to then, and based on that, Sophia will make a recommendation on how to proceed from there (which you can ignore without consequences). This is the point at which the stories diverge, as you will get three answering options; you prefer the journey together with Sophia, you prefer to think your way through, or you prefer to fight your way through. Your answer determines the 'path' and the corresponding story you will take from there:

When you say you prefer the journey together with Sophia, Indy will take the 'Team Path', which involves challenges that require collaboration between Indy and Sophia. This journey will take them to Algiers, Monte Carlo, Crete, and a trip by submarine to Atlantis, where Sophia will be kidnapped by the Nazis upon arriving there.

When you say you prefer to think your way through, Indy will take the 'Wits Path', which involves challenges that require thinking and puzzle solving. This journey will take Indy to Algiers, Monte Carlo, Thera and Crete, and a trip to Atlantis by an Atlantean tram. The Germans have already arrived with Sophia as their prisoner when Indy arrives.

When you say you prefer to fight your way through, Indy will take the 'Fists Path', which involves challenges mostly solved by fighting or other physical efforts. This journey takes Indy to Monte Carlo, Algiers, Crete (where you pick up Sophia), Thera, and a boat trip to Atlantis, during which Sophia will be kidnapped by Nazis again.

The three storylines converge at the point where Indy enters the outer ring of Atlantis, the rest of the story follows the same script, regardless of which path you took before.

Yes, there are. As explained above, the second act of the game is variable, the third and final act is the same for all three paths. However, depending on your actions in the third act, several different endings can be triggered.

Regardless of which path you took, when you enter Atlantis' outer ring, Sophia has been kidnapped by the Nazis and locked in the dungeon. You can save her by defeating the Nazi guarding her (by fighting him or crushing him with the Atlantean statue), handing her a metal pin, lifting the prison gate, and having Sophia brace the door with the pin. In the inner ring, in the sacrificial room, Sophia will be possessed by Nur-Ab-Sal who is housed in her necklace. You have to save her again, by putting a orichalcum bead in her necklace and put it into the gold box, which will prompt Indy to throw it into the lava, kill Nur-Ab-Sal and save Sophia. At the end, Dr Ubermann will force Indy to try the Collosus Machine. Convince him that you will get back at him if it works; Ubermann will take Indy's place and die. When this is all done, Indy and Sophia will escape, and watch Atlantis become a volcanic eruption from the top of the submarine, and have a romantic moment.

Should you fail to release Sophia from prison, OR if you leave her in the sacrificial room, possessed by Nur-Ab-Sal, and you persuade Ubermann to try the machine, then Sophia takes his place, kills him and dies herself. Indy will escape Atlantis and watch the eruption alone, lamenting Sophia's stubborness.

Should you fail to convince Uberman to take your place on the pedestal, then Indy becomes a god, kills Ubermann, and then dies himself, regardless of what you did with Sophia. This is not a real ending, though, as the game will conclude with a text screen, which also appears earlier in the game when Indy dies or loses a hand-to-hand fight

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