She turns up in Superman/Batman, and then gets her own title for a while which is basically her first trade. After that, Infinite Crisis hits and she sees Superman before heading off into space with a group of heroes (think that's reprinted either in a Superman trade or that second Supergirl trade). At the end of Infinite Crisis, there's this great big rift in space/time out in space, causing various effects - two heroes get merged together, Hawkgirl ends up 50 feet tall and Supergirl vanishes into the time stream and turns up 1000 years later with the Legion.

She spends however long with the Legion but eventually is sent back to our time, appearing during the World War Three seqments of 52 (the weekly comic telling the story of what happened during the missing year before One Year Later). After that, she and Power Girl go off into Kandor and your trade resumes. So basically, she was missing for 50 weeks before she came back.

You think this is bad to work out - I'm basically keeping a running checklist of what goes where for Countdown - which is weekly!