While solving the third case, after Athena inspects the dead body, Phoenix says "Nice work, Athena. Your face only turned five shades of pale. I was expecting fifty." This is a clear reference to the title of the popular romance novel.
In Case 2: Monsterous Turnabout there are afew references to "Nine-Tails" and people will make comments to the order of "It was sealed away" and "It caused devastation." The nine-tailed beast also resembles Nine-Tails, the character from Naruto.
Complete the DLC episode Turnabout Reclaimed to unlock the Phoenix's "Nostalgic" outfit to wear in-game. This is the same outfit that Phoenix wore briefly in the Third game in the series: Trials and Tribulations.