Let me say what I’ve found out so far. Marina says how “the safeguards in place to protect the soul's owner” were tampered with. And in her Dev Diary she says how she’s going to ask “that person Cuttlefish introduced her to for help”.
We know she’s talking about Agent 4 because of the conversation we get from opening the first locker.
Reading Agent 4’s palette after beating the tower with it, we get more information that confirms that Marina in fact wants Agent 4 to be the Memverse security. We see how Smollusk mentioned that Agent 4 is strong and that “Buuut...no weason such stwength shouldn't be used to pwotect a world of order”. This information is important for a reason and this leads me to the last bit of information I have.
The boss fight “Parallel canon”. Why is this fight important? Because it shows us a robot version of an inkling. But it’s not just any old inkling, it’s agent 4.How can we know this? Just look at the icon for the boss and the robot in the middle. It has Agent 4’s hairstyle with the hero shot as the weapon it uses. Not only that but if you have Splatoon 2, the hairstyle you pick for Agent 4 will show up on the main inkling robot. I fought the boss multiple times and it always had the hairstyle I chose for Agent 4 in Splatoon 2.
So there’s no exact reason what happened to Agent 4. They could be hanging out in Inkopolis Square somewhere or they could be the robot in the “Parallel Canon” fight. All I hope is that we get more info on what’s going on with Agent 4 because they seemed to have an important role of being the Memverse security