When the Dalek Restoration Empire appeared to fall to the Entity, the Emperor of the Restoration came to Mechanus, proposing an alliance to the Queen. Taking the Emperor to the city's star chamber, the Queen reviewed the progress of the Entity before Mechanus' defence grid began failing. After witnessing her guards destroying his Silver Dalek entourage, she noted the lack of reinforcements and wondered if he and the Prime Strategist truly were the only Daleks left. When the Mechanoid City's power was suddenly drained, the Emperor revealed that he had deliberately led the Entity to Mechanus. (WC: Planet of the Mechanoids) As the Mechanoids defended against it, the Queen made clear she was considering the Entity's demand to surrender the Emperor and later left him out in the open as the Entity broke through.
After the Strategist and Mechanoid 2150 sent the Entity back to the dimension it came from, the Queen ordered the Daleks to leave Mechanus. She promised that the Mechanoids bring an end to the Daleks. (WC: The Deadly Ally)
The Queen led the Mechanoids into the Dalek City, intending to destroy it. They were met by the Emperor, who revealed the Daleks weren't as weak as they had been led to believe and unleashed an army of Silver Daleks against them. During the ensuing battle, the Queen and 2150 found the Strategist and tried to convince him to turn on the Emperor. He pretended to agree and the Queen helped escort him through the battlefield to another chamber. When the portal to the Entity's dimension opened above Skaro, she proclaimed that the Daleks were finished. However, the Strategist betrayed the Mechanoids and sent all of them on Skaro through the portal, including the Queen. (WC: Day of Reckoning)