Can a marriage be annulled or declared void , if wedding ceremony was done ?

A divorce petition cannot be entertained until the completion of one year from the day of marriage.

To file a case for dissolutuion iof marriage by a decree of divoce on the grounds of mutual consent, the parties to the marriage should have live separately away from each other for a minimum period of at least one year hence it is not possible to file a mutual consent divorce case now.

An annulment petition can be filed within one year from the date of marriage if the marriage is not consummated  and this petition cannot be filed on mutual consent because this can be considred as collusion between the parties hence not valid in law. 

if she is not willing to live with you and you think there is no future from this marraige then certainly the Mustual divorce is the only best option

In this situation it is necessary to understand the essential difference between annulment, nullity and divorce under Indian law. 

When there is legal declaration that a marriage never existed is Nullity of marriage.  When a marriage from the beginning is deemed void due to specific legal violation as mentioned under the Hindu Marriage Act, 1955 Sec 5 such as:

Either of the party being within prohibited degree of relationship.

Either of the party being of unsound mind during the marriage 

Either of the parties being 

Whereas the legal procedure that declares a marriage voidable is annulment, that means the marriage is initially valid but could be annulled on specific grounds like:

Mental incapacity

Either of the party being impotent

Lack of consent due to coercion

In your situation as stated you were married three months ago and then your wife returned to her parents after only two days, there are various avenues you can explore:

Since she is seeking for divorce under mutual consent it is a straightforward option, as the parties can file for divorce which will be granted for a stipulated waiting period, for around six months; unless waived by the court.

File a petition in court if you feel there are grounds for annulment i.e. if there is coercion or lack of consent. You need to prove this specific ground under the Hindu Marriage Act sec 12. If the marriage does not fall under the category of void marriage, then you can file a declaration for nullity. For this you need to demonstrate that the marriage did not meet the legal requirements at time of the ceremony.

The simplest route is filing for mutual divorce, if both parties agree ensure that the parties understand the terms with regards to financial settlement. If you feel that annulment is no valid points then discuss it with your lawyer to further filling a petition in court. Collect any evidence if pursing annulment or nullity, to support your claim. The fact that your wife did not cohabit with you and the wedding ceremony took place as well is now seeking a divorce, opens several legal avenue. 

"my wife stayed with me for only 2 days"! Has the marriage been consummated?

"never returned(for her personal reasons)" What are those personal reasons, at least to your knowledge?