Mission 3 commences once you hit Level 5, and you will be directed to Manhatten. When you land Lonnigan, will show up again, telling you about a problem within Liberty, and to get out while you can. When you enter the bar, the bartender gives you a message to meet Juni at California Minor. Sell any collected silver here, and purchase H-Fuel as much fuel as possible, then head to your destination.
When you enter the California system, a survivor from Freeport 7 will also try talking with you, but will be destroyed by three navy ships. The ships quickly destroy the target (and should you decide to engage, can kill you in only one volley). However, engaging them (and killing at least one of them) yields a nice bonus in for of a turret drop - Rowlett's Revenge (lvl. 3 laser), 37/18 dam, 8.33, 700/700, 7 energy. When they start firing their missiles at you just keep some distance, fly some turns and continuously drop decoy, they'll quickly run out of ammo and are sitting ducks by then. Continue to the waypoints to California Minor. When you land, you can accept the mission from Juni; followed by hearing a news broadcast about Lonnigan.
If you have difficulty with the next section while piloting a freighter, California Minor provides an acceptable price for the H-Fuel, which may be sold in exchange for a more suitable ship.
Take the trade lane to San Diego, and catch up with the convoy. The artifact convoy will be ambushed at the third waypoint by Outcast Heavy fighters. After the battle, you get the chance to dock at Willard, where you can sell the H-Fuel and purchase a new shield and other equipment. Continue to California Minor; where you will encounter three Reinland military vessels en-route. Destroy them, and proceed to the bar.
After chatting with Walker, launch to space and meet up with him. At this time, the Willard outpost will come under full attack by Reinland military. Enter formation with Walker and join the combat. The priority targets are the Bombers, which will attack the friendly cruisers (part of your pay), and the Gunships (which are too fast for the cruisers, and have no shields.) Once they are destroyed, the mission is complete.
Interlude[edit]
When you land you'll be at Level 6, so you can buy Class 4 weapons/shields and Razor mines, though you can't find a Class 4 shield in Liberty. Go ahead and explore the California and Texas systems now. After you start Mission 4, you won't be coming back to Liberty for a long time. There's a Junker base in NW Texas and a Rogue base in E California; you can use the Patrol Path map to find them.
If you are so inclined, now might be a good time to try your hand at piracy. You probably want to confine yourself to preying on the Liberty corporations: Interspace, DSE, Ageira, Universal and Synth Foods, since they like you a lot and will hate you as of Mission 4. Just shoot a trade lane out in the middle of nowhere until it breaks and then blow up transports that come by. Apparently with trains and heavy transports, you can just shoot off the cargo tanks instead. It'd take a lot of piracy to make them hate you.
Another approach to piracy is looting Storage Depots. The middle one near Manhattan contains Polymers, which sell for $491 on Denver. One of the depots near Fort Bush has H-Fuel, which sells for $360 on Manhattan ($425 California Minor). Note that if you leave the system and come back, the locals will forgive you.
If you just want to trade, running Beryllium from LA to Pueblo Station makes $180 each. On the reverse trip, (H-Fuel from Planet Denver @ $279 sells @ $425 @ California Minor or $444 at Willard) , Superconductors earn $79.
Before you hook up with Juni again, pick up some Engine Components at Houston. You can make $824 each selling them during the next mission.
By this point, you may have annoyed enough other people that the Xenos feel positively towards you (i.e. the bar goes to the right). If so, you could visit Ouray base and buy some of their excellent guns.