My 2004 chevy malibu will not start. we have replaced the starter and the starter relay fuse. we have taken the battery to be tested and it is cranking exactly what it should be. the lights and radio come on, but instead of turning over it just clicks once and nothing else

Is the vehicle security light lit ? It could be a fuse or the starter relay , or even the ignition switch , or even the PNP - park neutral position switch . This is a complex electronic starting system , computer controlled . The ignition switch is a low voltage input to the the BCM - body control module . When the BCM receives this input to crank the engine a lot of complex commands are sent over the serial data network to the PCM to enegrize the starter relay , there by sending battery voltage to the S terminal on the starter solenoid . If your mechanic disconnected the battery it could have caused the radio to say locked , you need a code to enter into the radio to unlock it , may need to have the dealer hook up their factory scan tool to do that .
Your best bet , find a better automotive technician , not a mechanic.
Circuit Description (Key Start)
For ignition switch power modes refer to Body Control System Description and Operation in Computer/Integrating Systems. Once the ignition is placed in the Run/Crank position, the control circuit of the Run/Crank relay is grounded by the body control module (BCM). With the Run/Crank relay switch closed, battery positive voltage flows through it and on to the park/neutral position (PNP) switch. With the PNP switch in either the Park or Neutral position, battery positive voltage will flow to the starter relay coil supply voltage input terminal of the powertrain control module and the coil side of the starter relay. Placing the ignition in the START position sends a message to the powertrain control module (PCM) requesting engine start. If the PCM has determined that the transmission is in Park or Neutral and theft is not active, it will ground the control circuit of the starter relay. Battery positive voltage will then flow through the switch side of the starter relay to the S terminal of the starter solenoid, cranking the engine.

Ignition switch, anything in the starter circuit including fuses, relays, connections, neutral safety switch, connections on starter, starter itself .

I don't know what testing you have done, as far as wiring circuits? You can see the starter fuse in the diagram, not only check the fuse, check for voltage on the fuse circuit, use a test lite to check for voltage. At the starter motor itself, two voltage circuits, one hot all the time, the other goes hot when starter relay is energized. Check those voltage circuits. The starter motor grounds through engine block.
You can unplug starter relay, use proper jumper wire, between terminals 30 and 87, the starter motor should crank the engine. If you try that, make sure tranny is in park or neutral and parking brake is set.

Dealer ship parts department.

Before you do any thing check for loose or bad connections. Also check you ground connection to engine. Check Fuses, relay and for a Fusible Link open circuit. Now let me explain what a Fusible Link does. They are short lengths of small gauge wire installed between the Battery and the Ignition Switch, or the Battery and the Fuse Panel. They'll melt and open the circuit before damage occurs in the rest of the circuit. I hope this was helpful you.

check the auto shutoff relay it controls both spark and fuel..

You can use some tool to check your car. Car Diagnostic Tool

This vehicle is 13 years old. Determine if it is feasible to tow it in and have it diagnosed to fix the problem.

I would start by checking all the fuses. Check your wires to your battery. If your turning the key and hearing nothing, probably a starter or battery. If it cranks, could be the ignition system.

You will need to Check the Fuel Pump and Relays, and also Change the Fuel Filter. There is a Fuse Relay Box under the Hood that has the Fuel Pump Relay in it.