The Ninja 250 has a basic, fluid-based cooling system, composed of a water pump, a radiator, a thermostat, an electric fan, and an overflow tank. There are also tubes which interconnect the various pieces. Some are built into the motor as coolant passages, and others are external hoses of metal or rubber. For a good overview of how an engine cooling system works, please see this article at howstuffworks.com. A Ninja 250's cooling system is conceptually identical to a car system; it's just smaller to match the smaller engine.
In normal operation, assuming a system in correct working order and filled with coolant, the engine will remain at the correct operating temperature almost entirely through natural convection, as air moves past the radiator. The air moving past the radiator carries away heat, removing it from the engine. In some circumstances, the cooling system either doesn't receive enough air, or doesn't receive cool enough air, and it will engage the electric fan. This typically happens when the air temperature is over about 80° F (27° C), or when the bike is stopped or moving very slowly.
Another important part of the cooling system is the thermostat, #49054 in the diagram:
The thermostat feels the temperature of the engine and decides how much cool water it should be fed with, in order to keep the engine temp stable. The thermostat keeps a minimum flow of water into the radiator while the engine warms up. This helps bring the engine up to proper operating temperature more quickly. (That's a good thing.)
After the engine reaches the proper temperature of operation, the thermostat opens gradually, but only enough to keep that temperature in the engine constant, avoiding over-cooling. If the cooling of the water in the radiator is not enough, even when the thermostat is fully open, then the electric fan starts.
This schematic shows the components of the Ninja 250 cooling system and how they relate to each other.
Things to note on this drawing:
1. The radiator cap does more than just keep the coolant inside. It also adds extra pressure to the system, thereby raising the boiling point. Without a radiator cap, the boiling point of a 50:50 coolant and water mix is barely more than that of plain water. But add a typical 15 psi cap and the coolant doesn't boil until 265F.
2. The direction of flow of the coolant is from the upper right hose to the lower left. You can see that the coolant temperature is significantly lower when it exits the radiator than when it enters. (T equals coolant temperature in these measurements.)
3. The fan comes on when the coolant gets above about 225F. It stays running until the coolant temperature falls back below 205F.
4. At 10,000 rpm, the water pump pushes the coolant through at eleven gallons per minute, which means that the single quart of liquid in the system is (theoretically) doing a circuit 40 times a minute. Be kind to your hard-working coolant and change it regularly.
Reading the temp gauge
The "correct operating temperature" is any temperature between the second low mark and the bottom of the red zone, which are connected together by an arc line. If the gauge shows colder than the second low mark after the engine has been warmed up, or into the red at any time, that indicates a problem with the cooling system. Additionally, the bike's temperature will tend to run hotter during stop-and-go traffic and cooler out on the open road, due to the cooling effect of the wind.
The fan engages at a predetermined point on the temperature gauge (they're not actually tied together in the sense of using the same temperature sensor, though). Many bikes engage the fan just below the red zone, while others have been reported engaging the fan at the mid-way point on the temperature gauge. The most important thing here is that it's entirely normal for your bike's temperature gauge to run all the way up to the bottom of the red zone before the fan comes on.
For more information on troubleshooting the cooling system, please read this article.
A useful analogy
To properly understand how heat and cooling works in the engine, think of the engine as a water tank, and heat as the water. In this analogy, the radiator and cooling system are the drain pump, getting rid of excess water. The more air you've got flowing over the radiator, the more drain pump power you've got.
As you tootle along at a sedate pace on a residential street, your engine is generating a small amount of heat -- pouring water into the tank. The drain pump is more than large enough to get rid of any excess water. As you go faster, the engine generates more heat, filling the tank faster. The drain pump is still up to it, including absolute top-speed on a hot day. However, the tank gets fuller the faster you go, storing more heat energy in the engine. The cooling system can still get rid of enough heat to keep the engine in the right range, but that's about it. The tank fills to a good level, but doesn't overflow.
Now, imagine you get off the freeway and pull up to a stoplight. Your heat/water tank is full, because you've been generating a lot of heat driving fast. The cooling system was able to drain off enough heat to keep things under control as long as you were moving, but the tank filled up in the mean time. Now that you're stopped, the air flowing over the radiator is reduced to zero (which means your drain pump is down to zero pumping power). Suddenly, any excess heat at all (such as running the engine at idle) is enough to overflow the tank, because it's so full. The temperature gauge shoots up until the fan kicks in -- there's the drain pump stepping in at the last minute before the tank overflows. This situation (before the fan kicks in) is shown in the third diagram.
For a little extra reading on the cooling system, we suggest the following: