Bose's journey from Germany to Singapore by submarine was a well-remarked incident of World War II history. But what was the need for the Germans or the Italians to use a submarine to transfer a civilian? Was it impossible for them to arrange a flight? Or was it done to force Bose, whose relationship with Hitler was frosty, to make an uncomfortable and unsafe journey?
No, it wasn't possible to take a plane.
As I mentioned in the (currently accepted) answer to Which city was attacked by Nazi-German war flights in India during WW2? , the Nazis did not possess any plane capable of making a flight from German-controlled territory to India, much less Japan, without stopping for refueling, and they did not have any aircraft carriers.
Even so, airplanes in WW2 were not nearly as safe as they are today. Worse, they can be spotted, and if spotted in range of an enemy air field fairly easily taken down. This is, in fact, how the allies killed Admiral Yamamoto. So it is quite likely submarine transport would have been safer, even if air transport was an option.
In fact, the transfer to the Japanese sub occurred 10 days after Yamamoto was shot down. Its likely both Bose and the Imperial Navy wouldn't be inclined to risk another VIP that way so soon.
Bose was sent on U180, a specially built fast cargo submarine whose main role was to refuel other U-boats operating in the Indian Ocean, however its cargo also included three tons of Gold for the German Embassy in Tokyo, therefore the handover had several diplomatic aspects.
The Bormann Brotherhood, 1974 William Stevenson (former WW2 RN intelligence)
In fact Abwher parachutists were infiltrated by air into Afghanistan and these men were responsible for collecting Bose from the Khyber pass and leading him to Kabul where there was an airstrip used to repatriate him to Germany via Rhodes.
Some time later there was a flight to China made by the Italian Servizi Aerei Speciali using the SM 75 aircraft, "MM-60539." The original successful flight left via the Crimea at great peril so the second of these flights was proposed via the same airfield in Kabul.
Some Italian archives are available which detail this:
ACS, Ministero Aeronautica, Gabinetto, busta 69
Vol 9 Gabaereo to Ministero degli Affari Esterni November 13, 1942
Vol 10 Ministero dell' Aeronautica Appunto per il Duce November 13, 1942
Vol 10 Gabaereo to Stato Maggiore R.Aeronautica November 17, 1942
Vol 10 Gabaereo to Stato Maggiore R.Aeronautica December 1, 1942
There was no need to infiltrate Bose back into India as he was worth more to the Axis being sent back to Japan via the submarine base at Singapore to influence Indians in Malayan POW camps to desert and join the Axis cause