So Walter goes to talk to Aaron after Olivia fills him in on the artwork covering the tunnel's walls. "You never mentioned you'd been there before yesterday. Based on the size of your artwork, I'd say you go there a lot," says Walter.
A still groggy Aaron says it's hard to explain, but he would go there sometimes, just to get away, and then he'd start to feel better. Maybe he can go there now so he can speak at a normal rate again? Anyway, he says that he would feel like he wasn't alone, that there was something there that was sad whenever he was sad. He's reluctant to go on, feeling like it sounds stupid, but Walter encourages him to continue. "I guess I thought I was just imagining it. Maybe I was crazy. But it was like it understood me, like it wanted to protect me," he says, with Walter saying "...protect you" at the same time. Then, he gently asks if Aaron intentionally led the boys chasing him into the tunnel. Aaron starts to sob, saying he swears he didn't know what was going to happen. "I didn't know what it was," he says. Walter hushes him, saying he believes Aaron did nothing wrong, and then goes out to get in touch with Olivia.
Lee and Olivia are back in the lab, with Walter "explaining" that they're not dealing with colonies of fungi, but with a single organism with rapidly evolving communication skills, which allowed it to form a psychic bond with Aaron. Those orangey-yellow masses? Those are the equivalents of neurons, and the tendrils are dendrites and synapses linking them all together. Lee breaks it down for us: "You're telling me that this whole thing, all of it, is one big giant brain?" That's it exactly. Also, Walter has named it "Gus." You know, for the sake of clarity. I still think "brain fungus" is better. Anyway, that's why the colony in the lab didn't affect Aaron: it was only a mindless appendage that hadn't connected to the network yet.
So Gus can only make more of itself and is never going to meet a nice single fungus at work, so as it grows and becomes more evolved, it's more conscious of how ALONE IN THE WORLD it is, which is somehow why it forged a link with Aaron, and they've been spending all their time hanging out listening to the Cure and making plans to be roommates after Aaron graduates. Walter says that until they break the link with the boy, any assault on Gus will hurt Aaron, or worse.
But Olivia's phone rings. It's Broyles, with worse news about Gus -- there's been another attack, on a homeless man in Roxbury Crossing, which is six miles from the tunnel, directly above the Boston sewer line. "We have a major infestation on our hands. We need to eradicate this thing, and we need to do it now," says Broyles. Walter interrupts, anxiously saying he doesn't think Broyles understands that he hasn't found a way to brink the Aaron-Gus love connection yet.