No visa to destination country but can stay at stopover country? [closed]

Okay so I'm going to Tokyo from London and I'll be stopping over in Manila. Now my problem is, I wasn't able to get a Japanese visa. So my plan is to go to Manila instead. I'm holding a Philippine passport which I thought will be okay but then I remembered that they check the travel documents when you check-in. Because my flight is to Tokyo, will I be refused to board on the plane which is to Manila? What if I tell them that I'll be stopping in Manila and not take the Manila-Tokyo flight? Do you think there's a chance? I'm really worried so I hope someone can help me.