I'm currently in Atlantis right now, and I'm confused with this statement. There's "practically no story", but there's cutscenes, texts, and animated "weapons" that are technically storytelling. My main concern with those is the whole "excuses" thing being rather flimsily put when placed on the bigger picture, which can frustrate some folks. Me, for instance.
The starting element is fine. I guess there's really no need to explain why The Explorer went to Mesoamerica in the first place, or how he crashes. Goodness knows Indy movies tend to start with an initiating journey, no need to detail those. The connecting tissues between episodes on the other hand seems like a bunch of disconnected luck, both good and bad. The Explorer finds a random journal detailing the Soldiers' plans to capture the Professor in Egypt to find the key to Atlantis. What are they doing in Mesoamerica, then? I don't think there's any artifacts here that The Explorer recovers anyways that's relevant to the Atlantis thing, so it feels like a random stop the Soldiers took while traveling to Egypt that luckily told The Explorer about what to do next.
The Soldiers needs to find the Professor in order to nick the key to Atlantis. They couldn't find anything there, so they explored a temple complex to find it. So far, so good. They probably figured out what temple to look for based on the museum trinkets and documents. Easily handwaved. The capture and the second temple with the gate, still decent enough, though I can't for the life of me figure out why the Protectors don't just kill The Explorer right then and there or talk to him about what their mission are when he wakes up. Would've prevented pointless bloodshed with his escape.
The red guy is where I actually got a notch agitated. He tells me that the Soldiers have found a way to get to Atlantis anyways without the key. How did they do that? I know they used a sub, but how did they find Atlantis? Random diving? Would that mean the whole kerfuffle with the key and the gate have been a wild goose chase? Was there actually something in Mesoamerica that hinted at it that I missed? It just seems arbitrary to explain why they're there, but not how they got there. That alone would've been something, but then the red guy continued on.
He remarks that the Soldiers are foolishly harnessing the power of the undead, but then doesn't elaborate why they can't. If they can't 'cause they'll all be killed by the existing undead, then shouldn't the Protectors just wait it out and then seal the gate after? If they can't 'cause they'll unleash hell instead, thus needing to send The Explorer in to stop them, wouldn't it be a good idea to tell The Explorer about what it is and how to avoid it so he doesn't accidentally do that? I dunno, it just didn't sit right with me. Maybe it'd work if the Soldiers attack the temple that I was captured in and stole the key from the Protectors, having the u-boat later 'cause now they know where they are, but the current setup right now just weirds me out.