Optimus Prime, Megatron, Arcee, Bumblebee and Bulkhead traveled to the center of the Earth to destroy Unicron's spark. Eventually, Optimus and Megatron were inside the spark chamber while the others battle Unicron's antibodies outside. Unicron was able to control Megatron and nearly killed Optimus if it wasn't for Megatron trying to hold back. Optimus used the matrix to destroy Unicron's spark, thus putting Unicron's body into stasis.
It was revealed that Unicron survived, but his body was put into stasis.
Attempting to exact revenge against both Earth and Cybertron for their role in his perceived fall, Megatronus used a spark fuser to summon both the AllSpark and the remaining Anti-Spark of Unicron. The Anti-Spark consequently rose from Earth's core to Earth's surface, but after Optimus Prime destroyed the fuser, the Anti-Spark flew back down through the hole it had come from.