The relegation-haunted Gulls got off to a flying start with on-loan Notts County midfielder Joss Labadie heading them into a second-minute lead.
Top scorer Rene Howe took his tally to 16 goals for the season by doubling Torquay's lead in the eighth minute by deflecting on-loan Sheffield United winger Jordan Chapell's goal-bound shot past Tommy Lee.
Cook, whose side scored late on through Liam Cooper, said: "Our game plan and everything else went out the window in the first eight minutes.
"We knew Torquay would be fighting for their lives. We had them watched on Saturday at Southend and they played really well.
"Unfortunately for us we did not start the game in any shape or form. We were second best for long periods and we end up getting 2-0 down and it's hard to come back from that.
"We did give ourselves a little lifeline in the second half and, to be fair to the players, they did keep working at it and kept trying, but the game had gone by then.
"You could be here all night trying to work out why we made a slow start. The message to the players was how important the game was and how we wanted to get off to a good start.
"We did not start and if you don't start well you get punished, no matter who you are playing."