Once inside the tunnel, continue shifting until Kat mentions hearing a voice. Follow the marker to find a man, and use your stasis field to help him travel up the tunnel. Follow the marker and place in the flashing area.
Once the Nevi appear, defeat them to be able to progress. Continue upwards and defeat more Nevi to travel out of the tunnel. Keep following the marker until a cutscene starts, explaining what has happened in the time Kat has been away.