bio-energy, i'd suggest you to do PhD. you'll learn and earn better, plus you'll have a stable career. now, talking about money, if you are a good biochemist, you'll earn really good money with a PhD degree (75+k). i've no idea where tensed got those figures but they are not true for all PhDs. yes some PhDs like plain biologists and plain chemists may get that much, but biochemists, chemical engineers, genetic engineers, molecular biologists, etc are paid better. if you go straight work with your masters, you'll probably earn 45k or so. i'd rather do PhD w/ whatever stipend i'll get (25-35k depending on where you do it) and another thing- i don't want to be treated like a kid by my colleagues who have PhD. this might not be important for you, but it is for me. you might even think that all places aren't like that, but sooner or later, you'll start feeling like you are being treated like a kid, which you are as a matter of fact when you compare the experience a PhD and a MS has.
don't worry about how much you'll make now, spend nice 3-4 years doing PhD and after that you'll have many alternatives than you'll have with just a masters degree. and, not to mention, you'll earn better, have a stable job, reputation, and so forth.

about biotech scope in Nepal, if you are into plant stuff, there's a lot you can do back home. if you are into animal stuff, there's nothing to do.