" ... Thirteen Years Later " is the second episode of Millennium to have been written by Michael R. Perry , who had previously penned the second season episode " The Mikado " , and would provide a further three scripts in the third season . The episode was directed by Thomas J. Wright , who helmed a total of twenty @-@ six episodes across all three seasons . Wright would also go on to direct " Millennium " , the series ' crossover episode with its sister show The X @-@ Files .