During the "Year That Never Was", she feared she had lost her son in the attack. Tom Milligan took Martha Jones to her lab, where she asked how Martha was going to defeat the Master. Martha said that she had a gun loaded with chemicals that could kill the Master despite his ability to regenerate.
When Martha and Tom left for London, she used a secret video link to the Valiant, the Master's base. She told the Master the whole plan in exchange for information about her son. This however was planned for by Martha; the resistance knew that she was a possible information leak.
When that version of 2009 was erased, time was restored to a different line. Alison did not know why Martha gave her a gift of flowers as a way of saying thanks and that she didn't blame her.