We present a spectral study of the ultraluminous Be/X-ray transient pulsar Swift J0243.6+6124 using Neutron Star Interior Composition Explorer (NICER) observations during the systems 2017--2018 giant outburst. The 1.2--10~keV energy spectrum of the source can be approximated with an absorbed cut-off power law model. We detect strong, luminosity-dependent emission lines in the 6--7 keV energy range. A narrow 6.42 keV line, observed in the sub-Eddington regime, is seen to evolve into a broad Fe-line profile in the super-Eddington regime. Other features are found at 6.67 and 6.97 keV in the Fe-line complex. An asymmetric broad line profile, peaking at 6.67 keV, is possibly due to Doppler effects and gravitational redshift. The 1.2--79 keV broadband spectrum from NuSTAR and NICER observations at the outburst peak is well described by an absorbed cut-off power law plus multiple Gaussian lines and a blackbody component. Physical reflection models are also tested to probe the broad iron line feature. Depending on the mass accretion rate, we found emission sites that are evolving from ~5000 km to a range closer to the surface of the neutron star. Our findings are discussed in the framework of the accretion disk and its implication on the magnetic field, the presence of optically thick accretion curtain in the magnetosphere, jet emission, and the massive, ultra-fast outflow expected at super-Eddington accretion rates. We do not detect any signatures of a cyclotron absorption line in the NICER or NuSTAR data.
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