Phelps led the through the first three laps, before tiring to finish in 1 minute, 59.76 seconds. Conor Dwyer won in 1:59.49, and Chase Kalisz was second in 1:59.53.
Phelps, the 18-time Olympic champion racing in his third meet since coming out of retirement, swam the 200 IM for the first time since winning the event in the 2012 London Olympics.
Franklin won the 100 back in 1:00.99. Amy Bilquist was second in 1:01.44.
Dwyer wrapped up the Grand Prix Series points race to earn a $10,000 bonus and a one-year lease on a BMW. Arkady Vyatchanin, the 100 back winner in 54:34, was second.