Work out what kind of layover you have
Three details decide everything else, and they are worth checking before you start planning an outing.
Whether your bags are checked through to your final destination. Whether your two flights are on one ticket or two. And whether your onward flight departs from the same terminal you landed in, since NAIA's terminals are separate buildings connected by road rather than by an airside corridor.
If your bags are checked through, your flights are on one ticket and your onward departure is from the same terminal, you have the easiest version of this. If any of those three is different, subtract time from whatever plan you were considering.
Staying inside
The airport publishes its amenities terminal by terminal, and the list is more useful than most people expect when they are looking at six hours in a chair.
There are charging stations, including in departure areas airside, and free wifi in passenger movement areas. Medical clinics are located in each terminal, with the Terminal 1 and Terminal 3 clinics past the customs area as you exit to the arrival lobby, and the Terminal 2 clinic at the arrival level rotunda. Currency counters, banks and ATMs are listed by level, including several in pre-departure areas. Tourist information counters and concierge desks in the arrival lobby carry brochures if you want to plan the next leg properly.
Lounges, paid rest facilities and food outlets vary by terminal and by hour, so treat what you find as terminal-specific rather than assuming a service you used in Terminal 3 exists in Terminal 2.
Changing terminals
If your onward flight leaves from a different terminal, the airport's free inter-terminal shuttle is the intended way to move. It is for passengers with connecting flights, it runs around the clock, and you board by showing your onward ticket. Published boarding points are the Terminal 1 arrival curbside, Bay 19 at the Terminal 2 arrival curbside, and the Terminal 3 arrival level.
Allow more time than the road distance suggests. You will go through check-in and security again at the second terminal, and the shuttle's frequency has been described differently on different official pages, so it is not something to plan a tight connection around.
If you want to leave the airport
This is a real option, but treat it as a decision with conditions rather than a default.
Leaving means passing through immigration as an arriving visitor. The Bureau of Immigration handles non-visa-required tourists under an initial admission period, with extensions handled as a separate process, so check your own nationality's position before you assume entry is automatic. You will then go back through departure formalities for your onward flight, including check-in cutoffs that are earlier than most people plan for.
Then there is traffic, which is the part that ruins layover excursions in Metro Manila specifically. The road journey from the airport into the city and back is not reliably predictable at peak hours, and a plan that works on paper with a two-hour round trip can quietly become four.
Bags are the hidden constraint
If your luggage is not checked through, you are carrying it, and that changes what an outing looks like.
The airport's passenger guide names baggage storage concessionaires at Terminal 1 and at the arrival level of Terminal 3. What it does not publish is pricing or the maximum storage period, so those are counter questions rather than things to plan around in advance. If storage is not workable for your terminal or your timing, that is usually the answer to whether you leave.
A sensible layover plan
Confirm your onward terminal and whether you need the shuttle. Check whether your bags follow you or need collecting. Decide early whether you are leaving, because a late decision wastes the time you were trying to use. If you stay, find your terminal's charging points, get some pesos if you have none, and treat the check-in cutoff, not the departure time, as your deadline.
