He met with John Frobisher about the return of the 456 and the need to remove any record of the first time Britain met them. Rather than take control, he left the matter to Frobisher - including the assassination of witnesses - so he could deny involvement if anything went wrong. Officially, "I never knew". (TV: Children of Earth: Day One)
The next day, he met with Frobisher to discuss the crisis and made it clear to Frobisher that he would be blamed if things went wrong. Afterwards he went to look at the gas tank being made for the 456 on Floor 13 of Thames House. The tank was built for the 456 when the ambassador visited the next day. (TV: Children of Earth: Day Two)
Green addressed the nation the next morning, promising calm and stability. He did not have a high profile on Day Three, only being seen observing the 456 landing at Thames House from his office in Downing Street. He witnessed the negotiation between Frobisher and the 456. Green was reprimanded by General Pierce of the American military for trying to cover up the British government's prior involvement with the 456. (TV: Children of Earth: Day Three)
On Day Four, Green held a meeting of COBRA to discuss how to meet the 456's demands of 10% of Great Britain's children, Green made a decision to exempt any COBRA member's children and grandchildren, including his own. This — and his refusal to make extended family exempt — was used by Home Secretary Denise Riley to argue that since they were throwing out a truly random "lottery", they should hand over the lowest 10% of children in the school league tables. Green had John Frobisher arrange transport for this. However Lois Habiba was spying on the meeting for Torchwood and tried to blackmail Green into letting Jack Harkness's team "do their job". Torchwood's show of strength spectacularly failed when the 456 casually murdered the entirety of Thames House; an angry Green sneered, "Happy now?" at Habiba and continued with the plan. (TV: Children of Earth: Day Four)
On the day he agreed to give the children to the 456, Green had full control of the crisis taken from him and given to General Pierce, who oversaw the taking of the 10% of the children. During the day, he had Frobisher order a media stunt to encourage the cover story for the taking of the children — innoculations. Green later told Frobisher that his children would be taken and given to the 456 so that the government would be seen to have suffered. Frobisher killed himself and his family to spare them this fate. At the end of the day, Green was having a meeting in the Cabinet Room with Denise Riley and Frobisher's PA, Bridget Spears. Green commented on how the situation turned out "lucky" for him, as the American General Austin Pierce had taken over the operation and they could blame the child snatchings on him. Once he'd shown his first thought was to save his own skin, Spears blackmailed Green: she told him she had used the Torchwood contact lenses to record the day's events in the Cabinet Room, including Green's comment about being lucky. Green threatened to have Spears arrested but Riley let Spears go and implied that she would be taking over from him. (TV: Children of Earth: Day Five)
Behind the scenes
In the short story Education, Education, Education Brian Green is mentioned to have been Lord High Chancellor and covered up papers about Saxon. He is also mentioned to be no longer in Parliament by 28th February 2021.