Late in the game, the danger just sky rockets, for no reason what-so-ever. My agents are fine
Most likely you didn't have enough power to stop some event, or if you left it alone for a long time, enough agents died and were replaced that their power dropped (every time an agent dies, you lose a little bit more ability to fight than that agent was worth). Can you send me your save file? They are automatically backed up when you lose, and there's a button in the pause menu to open where saved files are located.