Later on in the series it is shown that she works for Mr. Braun who himself works for SERN.She is ordered to retrieve the IBN to prevent the gang from accessing the files of SERN and to arrest Rintarou,Hashida and Kurisu. She killed Mayuri due to her unimportance in the case. It should be noted that she had no clue who Braun was and communicated with him using text messages and referred to him as FB.
In one of the time streams that Okabe had entered, Moeka had hung herself after not hearing from FB for a few days. Okabe intially fought Moeka to steal her phone, and after seeing her kill Mayuri multiple times, was overcome with hatred to even punch her in the face to get her phone. after calming her down and convincing her to co-operate with him, they find out that FB stood for Fyodor Braun, a pseudonym for Yūgo Tennōji, the landlord. he shoots Moeka for being a "traitor", but then kills himself. In her dying moments, Okabe promises to fix things and save her.
In the end, she works for Mr Braun as his assistant, taking over Suzuha's role in the shop. neither her nor Braun are linked to SERN, and Okabe gives her an official Future Gadget Laboratory Badge.