You need to do hostage crisis before the bounty missions are available!
Credit to Wallless Fury
Ok, to get to the Bounty Hunter Missions:
1st you need 4 things. 10 Gold Bricks, 1 vehicle (c7m3du - Republic Gunship), and 1 Bouunty Hunter (5kzq4d - Jango Fett) and (2kef2d - MagnaGuard). Now that you have everything. From the starting point in the Hub, make you way to the lift, and take it down. once there head to the upper section, not the lower two. Use the 10 gold bricks to open the door and head up, at the T intersection head left to the lift to the Hangar.
2nd, In the Hangar use the panel to get the Republic Gunship or any other you have. Hop in it, and once outside make your way right towards the CIS (Droid) Command Ship.
3rd, On the droid ship you will need Jango & the MagnaGuard. Use the hub and Free Play a level with both controllers so you can select both. Now exit the level and once your back, head left. Use the MagnaGuard to raise the bridge. Once across head towards the screen and you should see a Bounty access panel. Use Jango to open it, and head in! Head left until you see another hub, the stage is where the Bounty Hunter missions are located.
Hope this helps everyone who has been looking everywhere like I did.
Mission 1- R2-D2
Switch to Robonio and access the port directly to your left at the start of the mission. Crawl into the crawl space for mini figures and head to the Right. R2-D2.
Mission 2- Yoda
Run past all three tanks and yoda will be hiding just to the left behind the third tank and in front of the silver brain.
Mission 3- Padme Amidala
Once again run past everything. When you come to the Y in the road go left. Then use Helios-3D(or IG-86) to access the protocol driod port. Go through the open door then to your right. Padme will be in front of the juke-box in the back left corner with her back to you.
Mission 4- Anakin Skywalker
Run to the second area. Jump to the bottom main floor. Use Cad Bane(or other rocket boost character) To jet over to the R2-D2 station and swith to a droid character to access it. Then switch back to cad bane and boost back over to the main area. Run over past the stopped train and jump to the next platform. Boost over to the platform where the grey crates(and soon to be R2-D2 station). Step on the red button switch to a droid character and access the R2-D2 station. Then back to Cad Bane and Boost back to the platform. Run to your left and boost over the gap to the next platform. Then run down and you'll run into Anakin.
Mission 5- Captain Rex
Run to the bouncing blocks and build the crane. Then use a shooting character to lower you to the bottom level.Then run up towards the flames and use Rocket boosting character to boost over the flames. Continue going left and you will see Rex in the far upper left corner.
Mission 6- Plo Koon
From the star go slightly left to the mini area jumper and head down toward the landing area (access it pressing y). Head to the Upper right hand corner and you should be able to see his lightsaber and hear him dueling with a droid blaster. NOTE: On the behind the opposite side of the platform where the Escape Pod is.
Mission 7- Aayla Secura
Head towards the second republic cruiser and fly towards the big command tower till there is a cut scene that has it fly off (You can hold down A to get there a little bit faster). Then land on the newly formed landing pad. Head to the Upper right of the screen where you see the gold bathrooms. She will be slight to the right of them. You should be able to see her lightsaber.
Mission 8- Obi-Wan Kenobi
Head to the landing platform at the front of the ship. When you land there should be a crawl space just to the left of your ship. Switch to Robonino enter the crawl space and head straight down to Obi-Wan.
Mission 9- Ahsoka
Head to the wreckage that you see behind you and slightly to the left. Jump up on the rocks behind it and start running left. Past the jedi symbol for cutting the wall you will need to make a few jumps to get to her.
Mission 10- Kit Fisto
Head down the main hallway and use Cad Bane to Rocket boost over the two openings in the floor. Continue up the stairs till you get into the well lite main room. Head to the left and rocket boost over to the bounty hunter station. Enter the room and continue left past the Pool Table.
Mission 11- Bail Organa
Kill the first four Senate Commandos that you see and then steal one of there hats. Head to the Senate Commando access port against the back wall and just to the left of the corridor you just came from. Destroy everything along the back wall with thermal detonators and melee attacks. After that go the back left bed jump on the bench to get up to the bed, this should cause some red building blocks to fall down. Repeat the process for the back bed on the right. Then proceed to build the blocks you just released. If done correctly the Blue Neon on the left should continue all the way across the back wall of the room. You've probably lost your senate commando hat by now, but no fear, you can grab one from the wall in between the two beds on the left. Head out of the room and further right to the next senate commando access port. Access the port and enter the room. You should be able to see bail in the back of the room, just run to him.
Mission 12- Waxer
Blow up the Silver column on the left with an explosive, than jump on the nearby rock and get the middle section of the same column, switch to Jango, jump and rocket pack than blow up the top part. Waxer should fall down than.
Mission 13- Commander Cody
Don't let the overwhelming number of droids distract you. Run to the center of the intersection then down. Once you run up the stairs head to the right and you will see Commander Cody standing on a Balcony just to the bottom right of the screen.
Mission 14- Commander Ponds
Enter the newly formed cave from the start and keeping following it around. When you see the first wall with gold triangles head left. As you keep going you will see a second wall of gold triangles. Just as you reach the top of the incline into the room with the second wall of triangles Commander Ponds will be hiding in an alcove immeaditly to your right. It is very easy to miss him you are trying to hurry.
Mission 15- Luminara Unduli
Follow to cave around until you come to a rock wall block your path. Throw some Thermal Detonators and keep going. Follow the path till you come the R2-D2 access port and switch to a droid Bounty Hunter to access it. Enter the new found cave and head left, you should see her almost as soon as you start moving left.
Mission 16- Eeth Koth
This one is quite simple. Turn to face the windows and keep throwing Thermal Detonators at it until he Pops out of his hiding hole and run to him.