Despite being known as the King of the Monsters, Godzilla struggled mightily against Mechagodzilla in Godzilla vs. Kong. In the MonsterVerse, Godzilla has proven to audiences that he can take down MUTOs, King Ghidorah, and now Kong, but the buck stops at beating his robotic counterpart, at least on his own.
Following his victory over Kong, Godzilla got caught in a battle with APEX’s secret weapon: Mechagodzilla. The mechanized Titan, who was apparently being controlled by King Ghidorah’s severed head, gave Godzilla all he could handle and more. He was about to finish off the current alpha with the same move that Godzilla used to kill the female MUTO in the 2014 film, but fortunately Kong came to the rescue at the last second. Thanks to their combined efforts, the two ancient rivals were able to turn the tide. In the end, Kong finished off Mechagodzilla with his axe, which had received a big power-up from Godzilla’s atomic breath.
It was Kong who did most of the work in the fight against Mechagodzilla, which raises questions about how the robotic Titan gave Godzilla (who beat Kong) such problems. The amount of difficulty Godzilla had fighting him can be partially explained by his intense fights with the King of Skull Island. He was dealt numerous injuries during their second fight, including a stab wound from Kong's axe. It’s understandable that Godzilla would be exhausted from all the fighting he was involved in, similar to the time he collapsed right after beating the MUTOs in his first MonsterVerse movie. Admittedly, Kong was tired, too, but he had at least had the benefit of being supercharged by APEX’s HEAV vehicle.
Godzilla notably lost a beam struggle when he locked his atomic breath with Mechagodzilla’s laser. It’s possible that Godzilla’s blast was weaker because he had already used up most of his reserve energy. It’s important to keep in mind that before the fight, he accomplished one of his most impressive feats ever when he fired off a blast of atomic breath from the surface all the way down to the Hollow Earth. It stands to reason that such a dramatic usage of his atomic power would have significantly drained him ahead of his showdown with Mechagodzilla.
Of course, not all of this can be attributed to Godzilla being battle-weary and low on energy. There’s also the matter of Mechagodzilla himself, who would have been a challenging opponent for Godzilla even if he was still at full strength. APEX’s Titan was fueled by the supremely powerful energy source that Kong and the human characters stumbled upon while in the Hollow Earth. If this power is as incredible as APEX believed it to be – and the fact that it’s able to sustain the Hollow Earth ecosystem suggests that it is – then it makes sense that it could make Mechagodzilla strong enough to force a team-up between two alpha Titans in Godzilla vs. Kong.