  We present the results of $^{12}$CO($J$=1-0) mosaicing observations of the cD
galaxy NGC 1316 at kpc-resolution performed with the Morita Array of the
Atacama Large Millimeter/submillimeter Array (ALMA). We reveal the detailed
distribution of the molecular gas in the central region for the first time: a
shell structure in the northwest, a barely resolved blob in the southeast of
the center and some clumps between them. The total molecular gas mass obtained
with a standard Milky-Way CO-to-H$_2$ conversion factor is $(5.62 \pm
0.53)\times10^8$ M$_\odot$, which is consistent with previous studies. The
disturbed velocity field of the molecular gas suggests that the molecular gas
is injected very recently ($<1$ Gyr) if it has an external origin and is in the
process of settling into a rotating disk. Assuming that a low-mass gas-rich
galaxy has accreted, the gas-to-dust ratio and H$_2$-to-HI ratio are unusually
low ($\sim 28$) and high ($\sim 5.6$), respectively. To explain these ratios,
additional processes should be taken into accounts such as an effective dust
formation and conversion from atomic to molecular gas during the interaction.
We also discuss the interaction between the nuclear jet and the molecular gas.
