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- "It's just... I told myself the world needs Clark Kent even more than I do. But the truth is, I was so afraid of losing you." - Martha to Clark, Hostage
When Clark gained the power of persuasion from gemstone kryptonite, Lois got affected by its magic and started preparing her marriage to Clark and called Martha to tell her the news. They discussed wedding dresses and Martha was happy for Lois to wear her old one. After the effects were reversed, Clark and Lois informed everyone of their cancellation. While Clark and Martha were talking on the phone, she asked him to tell Lois that she could borrow "it" again when she is ready.
During this period, Martha assumed the identity of the Red Queen and works to protect Clark, acting primarily against Checkmate. She consistently left behind a red queen chess piece as a calling card, in opposition to Amanda Waller's white queen.
When she came back to the Kent Farm with her new boyfriend Perry White she started to try and get closer to Clark again. When Clark, Lois, Martha and Perry were having dinner, Lois and Perry left. Her and Clark were torn. Later, she (as the Red Queen) had Lois and Perry meet her on a rooftop, but she managed to escape. When Clark (as The Blur) came and ripped the door off, she used Kryptonite on him to get him away. She also hijacked the Watchtower and made sure no one (not even Chloe) could get to the files on Clark.
As part of her attempts to counter Checkmate, she has Martian Manhunter destroy the Kandorian's DNA. She then meets with Maxwell Lord, to have him get into Tess Mercer's head to find information on the Book of Rao. She then follows Tess Mercer to the Luthor Mansion. She takes the Book from Tess and warns her to be careful which side she chooses in the coming apocalypse.
Before heading back to the U.S Senate, Martha was confronted by Clark about being the Red Queen. She then gives the Book of Rao to Clark and explained the significance of it and the Kryptonians.
Martha leaves behind a gift for Clark should he chose to stay on Earth. The package contains a new costume with The House of El family crest emblem. Clark also discovers that after Lionel's death, Martha inherited his Kryptonian library.