Zaman,
IOS XE is a different from the “traditional” IOS operating system in terms of its architecture. IOS XE still runs the traditional IOS, but it runs as a single process (daemon) within a larger linux operating system. Notice in your output, there is an indication of this (linux):
(X86_64_LINUX_IOSD-UNIVERSALK9-M)
So, “Version 03.12.00a.S” refers to the large linux operating system, while “Version 15.4(2)S0a” refers to the IOS version being run by the IOS daemon within IOS XE. Make sense?
Here’s some more info on IOS XE if you want to read about the new architectural changes:
http://www.cisco.com/c/en/us/products/collateral/ios-nx-os-software/ios-xe-3sg/QA_C67-622903.html