I don't write fanfic(not that I don't want/like to, is just I'm not talented) so I'm probably the least person to give that kind of advice...anyway, a general idea would be somebody framed her: she's been investigating something a couple of days or even the day before the murder/stealing and the bad guy uses some hightech software or whatever to change/replace the date from the day Lois was there to the date of the murder.
Or something simpler, somebody it's been paid to be a witness that she was there plus a camera image the back of someone resembling her, she'll be arrested to be interrogated, she was out of town with Clark to investigate another story but didn't tell anybody. So being undercover nobody can testify they were there and there were no airplane tickets because they asked Superman to take them there. Of course, Superman would investigate this 'witness', find he's been paid and Lois'll be free.
Hope it helps.
Carolyn
