There are three possible issues with your Fusion’s transaxle. The first is in the clutch/band packs; the second could be in the valve body, and the third could be a sticking solenoid. All of them mimic the operation of the others, though, they are very different.
The clutch/band packs are the devices that enable your Fusion to go through the gears in the proper order. As the transmission spins up to match the engine speed, the proper gearing is chosen and the proper clutch/band pack comes into play. If the device has been damaged or is excessively worn, then it may grab and clunk into gear as you describe.
If there’s a problem with the valve body, your Fusion will act in the same way. The reason it is likely happening is that the valving that is controlling the flow of transmission fluid to a gear may be sticking and the result is that the Fusion’s transaxle thuds when it goes into gear. The checkvalves within the valve body are little more than lightweight ball bearings that float in a partial enclosure that is held open by a light-pressure spring. In action, the fluid is directed to a specific gear and the pressure in the channel is kept low so the valve remains open; other channels have their pressures increased to they close. The added pressure presses the ball bearing against the spring, halting fluid flow. If the spring becomes worn, it can let the ball bearing bounce within its enclosure and the transmission will clunk into gear.
If the gear selection solenoid packs stick, then the action is the same. Each gear is controlled by one of two solenoids on or in the valve body. The way the solenoids are activated determines which gear is being chosen. For instance, solenoid switch 1 on solenoid 1 may select first gear, while solenoid switch 2 on solenoid 1 may choose second. Solenoid switch 1 on solenoid 2 may choose third, while solenoid switch 2 on solenoid 2 may choose fourth. To switch to fifth, solenoid switches 1 and 2 on solenoid 1 may activate; while sixth would be indicated by activating solenoid switches 1 and 2 on solenoid 2. Reverse could be indicated by activating all of the solenoid switches or leaving them open. If one of the solenoid switches is slow or sticky, then your Fusion will operate as you describe.
To find out the problem, you are going to have to take your Fusion to a well-equipped full service transmission shop where they can run a full set of OBD-II diagnostics to determine and repair the problem. The cost of the repair will vary with the device, but, in general, you are looking at spending between $800 and $1,800.