In the second hour of the finale, Tom and Lexi attempt to complete their mission after they find the bombs destroyed.
An Overlord ship overrides their controls and docks with their ship. It's the Overlord that Tom set on fire. He attempts to kill Tom and control Lexi. She claims she brought Tom to him and she's still on their side. While distracted, Tom uses the poison to kill Tom. While not looking the Overlord broke the ship's auto-drive.
On the ground, the Espheni launch a bomb on Chinatown that has the means to turn humans into Skitters. They fight back and for the most part make it out alive.
Lexi decides to stay on the ship and use it as a bomb to take out the power source. Tom goes on the other ship to head home. They say goodbye. The Volm show up and help by taking out the Espheni ships headed to take out Lexi and Tom. Lexi succeeds in taking out the power source. Tom is taking off track and on the ship in space.
When the power source goes out the Espheni weapons stop working. The humans may have an advantage.