At the end you chase lazarus to a dock in Tokyo and he gets into a helicoptor. Then your friendly helicoptor comes by and gives you some homing missles. Take out the helicoptor and win.
Then it shows you standing there and lazarus's helicoptor in flames falling to the water. Then in the water it shows a little submarine going under water. That was lazarus escaping.
At the end of Blasto, you shoot the giant metal head of Bosc (the head bad guy) in a pool of lava. Blasto goes over to him and sees him laying on top of the head. After trying to bribe Blasto to let him live, Bosc sets off the self-destruct. Blasto runs away and finds Bosc's spaceship, then he flies away real fast.
It proceeds to show Blasto puke after warp-speeding out of the fortress of Bosc. Blasto then talks to the chief or whatever and says he is done with the mission, End of the game. You can get a different and better ending if you get all 40 girls.
The last boss takes a fairly long time to knock down. If you
stick with the pattern, he will die. Just keep circling and
blasting him while raising your shields when you see his missiles coming.
If you have any Dougan bombs left, use them, but wait
until he is closer to being dead. Don't let him get too close or he will hurt you bad. After you beat the boss, You are treated to a beautiful cinema and some closure to the story.
Unfortunately, you gave your life to make Sorcerer One operational again.