In 2nd gear

Hydraulic pressure is applied to the 2nd clutch, then the 2nd clutch engages the secondary shaft 2nd gear with the secondary shaft.
Mainshaft rotation is transmitted to the mainshaft 4th gear splined with the mainshaft.
The mainshaft 4th gear drives the secondary shaft idler gear splined to the secondary shaft and the secondary shaft via the idler gear shaft idler gear.
The secondary shaft and the secondary shaft 2nd gear engaged by the 2nd clutch, and the secondary shaft 2nd gear drives the countershaft 2nd gear splined with the countershaft and the countershaft
Power is transmitted from the countershaft to the final drive gear, which in turn drives the final driven gear and the transfer drive gear.
As the final driven gear turns the differential assembly, power is transmitted through the transfer drive gear to the transfer output shaft that drives the transfer hypoid drive gear/shaft and the transfer output shaft (hypoid gear).
Hydraulic pressure is also applied to the 1st clutch, but since the rotation speed of countershaft exceeds that of 1st gear, power output from 1st gear is cut off at the one-way clutch.

Fig 1: D Position And S Position With Automatic Shift Mode - 2nd Gear
Courtesy of AMERICAN HONDA MOTOR CO., INC.