If you find an agent who knows how to work his GDS he will be able to filter flights in various ways. For a start he can filter it so that all the flights are on the same alliance. He can filter by specific points (more than one).
He should then be able to simply book the flights and provide a fare for that combination.
Despite the appearance of alliances interline agreements still exist. Even though they are in different alliances it is still possible to book an itinerary using (e.g.) United, Air France and British Airways. The fares that combine to make up an interline journey can be eye watering but it's worth checking. I say "fares" but somewhere there is a fare from (say) Nairobi to London that has a mileage attached to it (known as the maximum permitted mileage). Then you work out a different mileage for each leg of your journey and add them together. If the sum of the individual mileages is less than the maximum permitted you pay that fare from Nairobi to London and get the stopovers (which can be for days or weeks) "free".
There's more ways to price an air ticket than the internet knows about!