When I reviews Cave Carson Has a Cybernetic Eye #10, I joked that the cover suggested they were fighting Poison Ivy or Swamp Thing. But thinking about it some more, I think that would have some potential. It wouldn't necessarily be those two characters, but someone who considered themselves connected to the Earth. If we were opting for less antagonistic, the current Terra would be a good choice, since she's familiar with life above and below the surface, and is pretty level-headed.
Carson spent a lot of time tunneling under the Earth, going wherever he pleases, having adventures and facing danger and such. There's a lot of life under the earth's surface, a lot of ecosystems. Since Cave and his team don't always know what's up ahead, they can't always predict how their actions are going to impact things. Is there a bacteria from the surface they brought with them that nothing under ground has resistance to? Did a predator in a magma cave travel through a tunnel they created into a massive crystal cavern full or some floaty, luminescent lifeform? That's not unusual here, species finding a way to a new location because humans create a pathway of suitable habitat that ends up connecting to some distant place. Underground, especially in the early days, the crew of the Mighty Mole would have been operation almost blind. Everything they saw and met would be new, and it wouldn't be hard to screw up without realizing it.
And there's the part where IDX used Cave's travels as a jumping off point for a lot of their own exploration/exploitation of what's below the surface.
I don't think Ivy would be bothered by the tunneling per se; someone that invested in plants would know about how organisms moving through the soil help aerate it. But the likelihood of all sorts of unintended consequences from the exploring, the fact rare species might be endangered because the Mighty Mole disrupted a carefully sealed system and introduced external predators. More of humanity destroying the planet in what Ivy might see as being reckless greed. Whether that's accurate or not, and I don't think it would be for Cave, that would be Ivy's perception based on a lot of past experience.
The lack of sunlight might hinder Ivy a bit, so she might have to act against them on the surface. Either target Cave and his team during a return from a trip, or attack someone left behind to draw him up. Or maybe she could act through root systems, send those down after him.
I don't know how Cave feels about what's happened underground as a result of his crew's adventures. Obviously he wasn't pleased with IDX's actions, slaughtering the Mul'droog and releasing the Whisperer, but beyond that. . . Does he regret the exploration? It's how he met Mazra, so that's certainly a positive outcome, but how much does he know about what happened as a result of where he's been and what he's done? Does it eat at him, but he can't see a way to fix it, so that being confronted by someone accusing him of causing all kinds of harm leaves him agreeing? Or does he shrug at it as the cost of doing business? Can't explore under the Earth's crust without breaking some (incredibly rare) eggs.