Thunderhead happens across the submersible and attacks the vessel, inadvertently alerting a nearby Aircraft carrier to its presence.
Thunderhead attempts to crush the vehicle against its body. Another submersible intervenes, distracting Thunderhead long enough to allow the damaged submersible to escape its grasp.
When the damaged submersible is forced to surface, Thunderhead follows it and surfaces as Brawler Yukon is dropped into the area by V-50 Jumphawks. Thunderhead engages Brawler Yukon, its advantage over the Jaeger apparent as it knocks the Jaeger down into the water repeatedly until it smashes against the pillar of a bridge and damages it. Despite the damage indirectly caused by Thunderhead, the survivors of the submersibles are able to create a momentary support for the crumbling bridge pillar and the Kaiju is eventually killed by Brawler Yukon.
↑Joshua Hale Fialkov: "One of the cool things in the movie is the idea that as the Kaijus are evolving. Because we’re taking place before that, we don’t quite know they’re evolving. We’re still learning the rules, we’re still learning how they work, so they behave in ways we don’t expect, necessarily. My favorite is one called Thunderhead, that is super awesome, and one called Ragnarok. Those are the two I love the most in the book."