Basically what sunandshadow just said. It's okay to think about the beginning and the end but don't leave the middle parts out either.
Maybe the other scientist you saved is on your side maintaining your cover since he owes you for saving him. Then the military suddenly ambushes you two having found out about your powers. The two scientists make their escape with the other one also fearing the consequences of his lies but he goes his own path different from you.
Then you could run into the other guy again. Couple alternatives just to show you the possibilities you can use the other character for:
1. He tells you about his escape plan but as you go along he leads you into an ambush. Turns out he was caught by the military when he made his escape and now he's trying to buy his freedom by helping the military to catch you. Since you didn't have to hide it from him anymore, watching you use your superpowers daily made him jealous of you and he was also angry you wouldn't share your secrets in how to obtain them.
2. He made his escape successfully perhaps through hiding and taking big risks but turns out the military was just on the heels of both of you and while you were having a chat they caught up on you. You two join in a grand escape finale.
3. You find your scientist friend but something is wrong. He seems dark and confident and doesn't seem to be running. He found a way to repeat the experiment on himself in secret and has also gained the powers. Since you didn't have to hide it from him anymore, watching you use your superpowers daily made him jealous of you and he was also angry you wouldn't share your secrets in how to obtain them and now he will take his revenge in crazed power. Perhaps he could be more powerful than you but he has a weakness such as instability which you can use to beat him.