OK so your hydraulic brakes are mushy. This happens a lot on bikes that are left sitting for a long time, especially out in the rain. Water can infiltrate the hydraulic system, rusting up the metal bits and diluting the fluid. Remember that brake fluid is meant to be able to be compressed to a certain degree, and it resists compression a lot more than water. So, the more water in your system, the more compressible your fluid is, and the more energy is absorbed by the fluid rather than being transferred from the master to the slave cylinder. Hence, mushy brakes. Here is how to repair it:

1. First, make sure everything is connected and tight. Look for cracks in the line, or leaks, or seeping fluid. Repair/replace as needed.
2. Unscrew your bleeder valve, down at your brake caliper. Just a couple turns out should do it, don't take it out all the way. It should immediately start seeping fluid.  Now go back up to your brake lever on the handlebar, and give the lever a little squeeze. You should get a spurt of brake fluid out the bleeder. If it does, then go ahead and bleed the system until clear fluid comes out:

If no fluid squirts, and/or you are having a hard time getting the brakes to bleed, you may have a clog in your brake system. No worries, this can be repaired. You will need an air compressor with a trigger attachment, and a small piece of wire.
3. Take the whole thing apart. This includes the master and slave cylinder, brake hoses, banjo bolts, and connector brackets. Try to keep track of everything, lay it all out on a big piece of cardboard if you want. Remember that the metal ends of each brake line always have one crush washer on each side of them. If you lose one, it will leak, these are very important. They are replaceable if you do lose one.
4. Dump/shake all of the old fluid out of everything. Now first, start with your banjo bolts. These are the bolts that screw into your master cylinder and caliper, you will also find them at connections and splits if you have dual front brakes, for example. Use your compressor to blow them clear. If they will not blow clear, use your wire to pick them loose. Clean all of the rust out of them. If they are too far gone, replace them.
5. Now clean up your master cylinder and caliper. Blast the hell out of the master cyl with air, inside and out, cleaning out the little passageways. Take out the bleeder valve from the caliper, and blast that through as well. Make sure the bleeder valve's tiny little holes are not clogged, you can get in there with a needle if you have to. Send some brake cleaner through the caliper and push it all through with compressed air. Inspect the caliper piston. With the caliper disconnected from the brake line, you should be able to push in the piston by hand with some effort. If you cannot then it is seized and needs to be restored with a rebuild kit, or replaced.
6. Now it is time for the brake lines. You will have to be a little creative with your trigger tip to send air through, but it can be done. If the lines are too clogged or are starting to crack, best to replace them.
7. Now assemble everything back up again, remembering to pay close attention to the crush washers. Fill in some clean brake fluid, and bleed the system using the hand pump. If you did a good job, everything should bleed through.
8. If the system is bled properly but the brakes are still mushy, inspect it all for leaks, especially the caliper and any connection/junction. Finding none, the master cylinder may be at fault. Repair it with a rebuild kit, or replace it.

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