It is not officially planned, but it is likely that they will. You see at the end if you ever watched after the credits,(WARNING: RUINER) a phone call is recorded:

Yes sir, the entire unit was wiped out,

those two are still alive.

The vector?

Yes sir, FoxDie should become activated soon right on schedule.

Yes sir, I recovered all of Rex's dummy warhead data.

No sir, my cover is intact, nobody knows who I really am. Yes, the DARPA chief knew my identity, but he has been disposed of.

Yes, the inferior one was the winner after all......thats right. Untill the very end

Liquid thought that he was the inferior one. Yes sir, I agree completely. It takes a well-balanced individual such as yourself to rule the world

No sir, no one knows that you were the third one, Solidus.

What should I do about the woman? Yes sir. I'll keep her under survellience.

Yes, Thank You. Good-Bye..........

Mr. President.

You know who I think it is, Revolver Ocelot. It is his voice, he was still alive the last time you saw him, he took the disk the DARPA chief gave to you. The evidence tells that it has to be him. And I think the President ahs a lot to do with this. They just said that he is the third son. SOLIDUS. Maybe Snake is in for more trouble. But anyway, it is very likely they are gonna have a sequel!