UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13G

(Amendment No. 3)

Under the Securities Exchange Act of 1934

Genta Incorporated

(Name of Issuer)

Common Stock, $0.001 par value

(Title of Class of Securities)

37245M603

(CUSIP Number)

December 31, 2012

(Date of Event which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule if filed:

¨ Rule 13d-1(b)

x Rule 13d-1(c)

¨ Rule 13d-1(d)

Represents 133,549 Common Shares and 661,968,876 Common Shares underlying $661,968.88 of Notes (defined in Item 4 below) which can be converted into Common Shares to the extent that, after such conversion, the Reporting Persons would beneficially own no more than 9.999% of the Issuer’s Common Shares.

This Amendment No. 3 (“Amendment No. 3”) amends and supplements the statement on Schedule 13G initially filed on March 15, 2010 (the “Original Filing”), as amended on February 14, 2011 (“Amendment No. 1”) and February 14, 2012 (“Amendment No. 2”). The Original Filing, as amended, remains in effect except to the extent that it is amended, restated or superseded by information contained in Amendment No. 1, Amendment No. 2 or this Amendment No. 3. Capitalized terms used and not defined in this Amendment No. 3 have the meanings set forth in the Original Filing, as amended. This Amendment No. 3 is being filed to reflect the Reporting Persons’ beneficial ownership of the Issuer’s outstanding Common Shares as of December 31, 2012.

Item 4 is hereby amended and restated:

Boxer Capital, Boxer Management and Joseph Lewis each beneficially own 662,102,425* Common Shares. MVA beneficially owns 662,115,966* Common Shares.

The Common Shares beneficially owned by Boxer Capital, Boxer Management and Joseph Lewis together with the Common Shares beneficially owned by MVA represent 9.999%** of the Issuer’s outstanding Common Shares.

MVA has the sole power to vote the Common Shares it beneficially owns. Boxer Capital, Boxer Management and Joseph Lewis do not have the sole power to vote or direct the vote of any Common Shares.

Boxer Capital, Boxer Management and Joseph Lewis have shared voting power with respect to the Common Shares they beneficially own. MVA does not have shared power to vote or direct the vote of any Common Shares.

MVA has the sole power to dispose of the Common Shares it beneficially owns. Boxer Capital, Boxer Management and Joseph Lewis do not have the sole power to dispose or direct the disposition of any Common Shares.

Boxer Capital, Boxer Management and Joseph Lewis have shared dispositive power with respect to the Common Shares they beneficially own. MVA does not have shared power to dispose of or direct the disposition of any Common Shares.

As of December 31, 2012, each of Boxer Capital, Boxer Management and Mr. Lewis, had shared ownership of the $85,160.70 principal amount of the Issuer’s 8% Unsecured Subordinated Convertible Promissory Notes due September 9, 2013 (the “April 2009 Notes”), $31,680.41 principal amount of the Issuer’s 8% Unsecured Subordinated Convertible Promissory Notes due September 9, 2013 and issued on September 4, 2009 (the “September 2009 Notes”), $1,403,645.73 principal amount of the Issuer’s 12% Senior Unsecured Convertible Promissory Notes due March 9, 2013 (the “B Notes”), $1,324,525.21 principal amount of the Issuer’s 12% Senior Unsecured Convertible Promissory Notes due March 9, 2013 (the “C Notes”), $1,489,104.83 principal amount of the Issuer’s 12% Senior Unsecured Convertible Promissory Notes due March 9, 2013 (the “D Notes”), $2,473,242.17 principal amount of the Issuer’s 12% Senior Unsecured Convertible Promissory Notes due March 9, 2013 (the “E Notes”), $1,436,704.28 principal amount of the Issuer’s 12% Senior Unsecured Convertible Promissory Notes due September 9, 2021 (the “G Notes”), $96,000 principal amount of the Issuer’s 12% Senior Unsecured Convertible Promissory Notes due September 9, 2021 (the “H Notes”), and $562,500 principal amount of the Issuer’s 15% Senior Unsecured Convertible Promissory Notes due September 9, 2021 (the “I Notes”, along with the April 2009 Notes, the September 2009 Notes, the B Notes, the C Notes, the D Notes, the E Notes, the G Notes, and the H Notes, each a “Note” and collectively the “Notes”). Boxer Capital held, in the aggregate, $8,902,568.33 principal amount of the Notes. As of December 31, 2012, MVA had sole ownership of the $182,264.18 principal amount of the B Notes, $167,142.84 principal amount of the C Notes, $160,824.39 principal amount of the D Notes, and $267,479.66 principal amount of the E Notes. MVA held, in the aggregate, $777,711.07 principal amount of the Notes. The Notes are convertible at a conversion price of $.001 per Common Share and can only be converted to the extent that, after such conversion, the Reporting Persons would beneficially own no more than 9.999% of the outstanding Common Shares.

Not Applicable.

(c) By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were not acquired and are not held for the purpose or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.

SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Exhibit 1

JOINT FILING AGREEMENT

The undersigned hereby agree that the Statement on Schedule 13G, dated February 12, 2013, with respect to the shares of Genta Incorporated’s Common Stock, par value $0.001 per share, is, and any amendments thereto executed by each of us shall be, filed on behalf of each of us pursuant to and in accordance with the provisions of Rule 13d-1(k)(1) under the Securities Exchange Act of 1934, as amended, and that this Agreement shall be included as an Exhibit to the Schedule 13G and each such amendment. Each of the undersigned agrees to be responsible for the timely filing of the Schedule 13G and any amendments thereto, and for the completeness and accuracy of the information concerning itself contained therein. This Agreement may be executed in any number of counterparts, all of which taken together shall constitute one and the same instrument.

IN WITNESS WHEREOF, the undersigned have executed this Agreement as of the 12th day of February, 2013.