I agree that the episode is well placed in the overall season's plot structure. We have Ellie and Joel embrace their strong personal connection after their earlier confrontation. We see them more relaxed with themselves and each other and settling into a Father-Daughter/mentor-mentee dynamic instead of the more adversarial one they had earlier. Pushing the other away to mitigate the pain of loss or failure in the mission, more so on Joel's part, but still. The Mentor, Protector, and Father is on the verge of being snatched away from her, so soon after Joel embraced this role, which resonates strongly with the unfortunate timing of Ellie's first kiss: elation at her romantic feelings being reciprocated, then devastation as the realities of the world they live in snatch that happiness and potential romance away from her. She's having literal deja vu, seeing the only person she cares for in this world dying in front of her, feeling powerless (she literally says something like I can't do this without you)...until she says eff that, I'm going to save you, or at least try. This is different than her relying on Joel for protection and guidance, which was a role previously held by Riley; Ellie is embracing her agency and trying to "save" that which she loves, instead of relying on their protection. But it's also different from the aggression and darkness that percolates out of her in the academy when she savagely beats the bully, which both hints that Ellie does not need a Protector and highlights the darkness that exists in her and Joel both.
Next episode will be interesting to see how savage Ellie becomes to protect her newfound Father. She's never been particularly innocent, having been trained for violence by FEDRA, but now she has someone to protect and I'm here for it.