If you wife is on a spouse visa then you will simply have to continue complying with the conditions of the visa until just before the visa expires.
Then, you will have to apply using form FLR(M) to extend her current visa. The visa will be extended for a further two years so that her total time in the UK by the end of the extended visa will reach 5 years.
Once she has reached 5 years in the UK on her spouse visa she must then apply for indefinite leave to remain using form SET(M).
Onve she has obtained ILR this means that she is free of immigration time restrictions which means that she can apply for naturalisation as a UK citizen by using form AN:
You will see that the above link contains the eligibility criteria to naturalise where the applicant is married to a UK citizen (ie. you). In particular, you will see that there a certain residential requiremnts about the limit of the amount of days that she can spend outside the UK in order to remain eligilble for naturalisation.
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