This episode feels more like a bridge episode between two seasons than a season finale. NGL, Secret Protocol set the bar very high in terms of thrills and sensations. And the teasers in trying to hide the most they could felt misleading to the fandom (the episode summary was on point though). Nonetheless, the episode notably reestablishes and summarizes all the consequences of Marinette's Secret™ about Gabriel this season.
Marinette sees what her actions with Adrien have leading him to : he is yet again living in his father's shadows. It wasn't her wish for him yet this is the result of her constant lies. She has gaslighted him into this false reality and she regrets it. Yet she cannot figure out how to untangle the multilayered mess she created. She is deep into an hole she dug herself and she doesn't see the light of the surface. At this point, no matter what her options are, she has also realized she will only hurt him and break his heart. And this is what pains her. Which leads me back to her dialog as Viper Bug in Mister Agreste - what happens when you are the one responsible behind the suffering and misery of the one you have sworn to protect at all cost? Do you truly get a second chance? Can you hope for forgiveness?
And surprisingly, they make a little parallel with the Gabriel's secret and her revealing her parents her super-identity. Now that they know the truth, they try to act chill but Marinette sees how worried they are about her. This is a permanent change from the season. With time, she might accept and welcome their support more, but right now, she regrets having told them precisely because they aren't blissed by ignorance anymore.
Same goes with Alya who has now figured out the truth and no memory erase spell can save Marinette this time around. In this episode Alya states clear boundaries between Marinette and her. IMO this is to me the best possible outcome. She will still help out if Paris is in trouble because that much is at stake (and that is why Alya is a A-ranking superheroine in my book). But Alya draws a line at what Marinette can use her for from now on. Cross that line again and they won't be friends anymore. And her line reminds us what Marinette made her do back in Lady Chaos. The episode gave the tone about upcoming Alya's interactions. Respectful but colder and distant for next season. So long Marinette's hasn't told Adrien the truth about his father.
Speaking of Alya, as Rena, she handled the team extremely well when LB was incapacitated. Even if it was part of the plan, Rena has material to be the leader of her own dedicated unit one day. (Again, linking back to Illustrhater ending).
For those mad that the episode had to spell it out that Chrysalis is a shapeshifter while it was obvious to the (older) audience, it wasn't for the characters. The new information is rather that Chrysalis is able to shapeshift consecutively. For us, I think it is safe to theorize that whoever was from that portal at the end of S5 finale gave her that power. And it might not be a Miraculous power either.
In Nemesis, Lila suffers her first real setback imo. It's the first time the Miraculers get that close to her. Although, they didn't do much further than that. The Butterfly Holder escaped and burn all the evidences in their lair. After this, it won't be surprising if the Miraculers won't get access to the Butterfly Holder for a long time. Lila will be more careful from now on. And so will the Miraculers now that they know about the Butterfly's additional ability.
Btw, it was nice for them to clarify that Marinette's secret protocol did work in the previous episode and truly bought herself time. Lila might not suspect her as being LB anymore, but she sure cannot help but be delighted and profit out of Marinette's misery has a little vengeance.