After you defeat the first incarnation of Zoda, you proceed farther into the alien spaceship.
Explore the Area
After you go west from the room where you first fought Zoda, go west under the metal wall and jump west to pick up the capsule. It will fully fill your health, and isn't temporary. Go west, then south to the next room.
Go west, and shoot the robot in the window while jumping over its bullets. When it's gone, go south and defeat the robot there. Then go west and kill or ignore the robot in the window. Go west to the next room.
If you don't want a laser gun, lightning gun, capsule, and magic potion, or if you already got them, skip to the next paragraph. If you jump on the tile when it's open, you will fall into a room with many robots, as well as a capsule and a laser gun. If you kill all the robots in this room, a north passageway opens, and you can go through it to get a lightning gun and a magic potion. These items will help a lot, so be sure to get them if you want them. When you're done, go through the east door and step on the teleport tile. You will be sent back to where you got the capsule right after you fought Zoda.
Jump on the tile when it's closed, then jump west and make your way west past the robots to reach the next room. You will reach the main engine of the spaceship.