SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 --------------- SCHEDULE 13D (RULE 13d-101) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) (AMENDMENT NO. 1) NEW YORK TIMES CO (Name of Issuer) Class A Common Stock (Title of Class of Securities) 650111107 (CUSIP Number) Barry Fink, Esq. Morgan Stanley 1221 Avenue of the Americas New York, NY 10020 (212) 762-7975 (Name, Address and Telephone Number of Persons Authorized to Receive Notices and Communications) July 17, 2006 (Date of Event Which Requires Filing of This Statement) If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), 13d-1(f) or 13d-1(g), check the following box. [ ] The information required on this cover page shall not be deemed to be "filed" for purposes of Section 18 of the Securities Exchange Act of 1934, as amended (the "Act"), or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act. ------------------- ------------------ CUSIP NO. 650111107 13D PAGE 2 OF 15 PAGES ------------------- ------------------ ------------- ---------------------------------------------------------------------------------------------------------------------- 1 NAMES OF REPORTING PERSONS I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY) Morgan Stanley IRS #36-314-5972 ------------- ---------------------------------------------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (a) [ ] (b) [X] ------------- ---------------------------------------------------------------------------------------------------------------------- 3 SEC USE ONLY ------------- ---------------------------------------------------------------------------------------------------------------------- 4 SOURCE OF FUNDS WC ------------- ---------------------------------------------------------------------------------------------------------------------- 5 CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) or 2(e) [X] ------------- ---------------------------------------------------------------------------------------------------------------------- 6 CITIZENSHIP OR PLACE OF ORGANIZATION The state of organization is Delaware. ------------- ------------ ----------- --------------------------------------------------------------------------------------------- NUMBER OF 7 SOLE VOTING POWER SHARES 8,411,277 ----------- --------------------------------------------------------------------------------------------- BENEFICIALLY 8 SHARED VOTING POWER OWNED BY 352 ----------- --------------------------------------------------------------------------------------------- EACH 9 SOLE DISPOSITIVE POWER REPORTING 9,541,084 ----------- --------------------------------------------------------------------------------------------- PERSON WITH 10 SHARED DISPOSITIVE POWER 352 ------------- ------------ ----------- --------------------------------------------------------------------------------------------- 11 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 9,541,436 ------------- ---------------------------------------------------------------------------------------------------------------------- 12 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES [ ] ------------- ---------------------------------------------------------------------------------------------------------------------- 13 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 6.62% ------------- ---------------------------------------------------------------------------------------------------------------------- 14 TYPE OF REPORTING PERSON CO, HC ------------- ---------------------------------------------------------------------------------------------------------------------- ------------------- ------------------ CUSIP NO. 650111107 13D PAGE 3 OF 15 PAGES ------------------- ------------------ ------------- ---------------------------------------------------------------------------------------------------------------------- 1 NAMES OF REPORTING PERSONS I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY) Morgan Stanley Investment Management Limited ------------- ---------------------------------------------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (a) [ ] (b) [X] ------------- ---------------------------------------------------------------------------------------------------------------------- 3 SEC USE ONLY ------------- ---------------------------------------------------------------------------------------------------------------------- 4 SOURCE OF FUNDS WC ------------- ---------------------------------------------------------------------------------------------------------------------- 5 CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) or 2(e) [ ] ------------- ---------------------------------------------------------------------------------------------------------------------- 6 CITIZENSHIP OR PLACE OF ORGANIZATION The country of citizenship is the United Kingdom. ------------- ------------ ----------- --------------------------------------------------------------------------------------------- NUMBER OF 7 SOLE VOTING POWER SHARES 8,105,895 ----------- --------------------------------------------------------------------------------------------- BENEFICIALLY 8 SHARED VOTING POWER OWNED BY 0 ----------- --------------------------------------------------------------------------------------------- EACH 9 SOLE DISPOSITIVE POWER REPORTING 8,957,570 ----------- --------------------------------------------------------------------------------------------- PERSON WITH 10 SHARED DISPOSITIVE POWER 0 ------------- ------------ ----------- --------------------------------------------------------------------------------------------- 11 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 8,957,570 ------------- ---------------------------------------------------------------------------------------------------------------------- 12 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES [ ] ------------- ---------------------------------------------------------------------------------------------------------------------- 13 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 6.2% ------------- ---------------------------------------------------------------------------------------------------------------------- 14 TYPE OF REPORTING PERSON IA, CO, HC ------------- ---------------------------------------------------------------------------------------------------------------------- ------------------- ------------------ CUSIP NO. 650111107 13D PAGE 4 OF 15 PAGES ------------------- ------------------ Item 1. Security and Issuer. ------ ------------------- This is the first amendment to the original Schedule 13D, which was filed on April 18, 2006. This statement relates to the Class A common stock, $0.10 par value (the "Class A Common Stock"), of The New York Times Company, a New York corporation (the "Issuer"). The principal executive offices of the Issuer are located at 229 W. 43rd St., New York, New York 10036. Item 2. Identity and Background. ------ ----------------------- The information set forth in Item 5 of the original Schedule 13D is hereby amended and restated to read in its entirety as follows: (a) This statement is filed jointly by the entities listed below which are referred to herein as the "Reporting Persons": (i) Morgan Stanley, a company organized in the State of Delaware ("MS"); and (ii) Morgan Stanley Investment Management Limited, a limited company organized under the laws of England and Wales ("MSIM") and is a wholly-owned subsidiary of MS. Principal business: (b-c) MS' principal business and principal office is located at 1585 Broadway, New York, NY 10036. MSIM's principal business and principal office is located at 25 Cabot Square, Canary Wharf, London E14 4QA, United Kingdom. MS is a global financial services firm that maintains leading market positions in each of its business segments - Institutional Securities, Global Wealth Management Group, Asset Management and Discover. MSIM is a wholly-owned subsidiary of MS. The name, business address, present principal occupation or employment and citizenship of each director and executive officer of MS and MSIM is set forth on Schedule A and B, respectively. (d-e) Neither of the Reporting Persons, nor to the best of the Reporting Persons' knowledge, any of the persons identified on Schedules A or B hereto has, during the last five years, (i) been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors) or (ii) has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws, other than, in the case of clause (ii), as described in Exhibit 1 hereto. ------------------- ------------------ CUSIP NO. 650111107 13D PAGE 4 OF 15 PAGES ------------------- ------------------ (f) The citizenship of MS is Delaware and the citizenship of MSIM is the United Kingdom. Item 4. Purpose of Transaction. ------ ---------------------- Item 4 of the original Schedule 13D is hereby amended by the addition of the following: The Reporting Persons are filing this amendment to disclose, as described below, that the Reporting Persons have purchased additional shares of Class A Common Stock. Item 5. Interest in Securities of the Issuer. ------ ------------------------------------ The information set forth in Item 5 of the original Schedule 13D is hereby amended and restated to read in its entirety as follows: (a) For the purposes of Rule 13d-3 promulgated under the Securities Exchange Act of 1934, as amended (the "Exchange Act"), MS may be deemed to beneficially own 9,541,436 shares of Class A Common Stock, or approximately 6.6% of the outstanding shares of Class A Common Stock. MS does not have any voting power over 1,130,159 shares of such Class A Common Stock. MS is filing solely in its capacity as parent company of, and indirect beneficial owner of securities held by, its investment management business units. For the purposes of Rule 13d-3 promulgated under the Exchange Act, MSIM may be deemed to beneficially own 8,957,570 shares of Class A Common Stock, or approximately 6.2% of the outstanding shares of Class A Common Stock. MSIM does not have any voting power over 851,675 shares of such Class A Common Stock. The Reporting Persons do not affirm the existence of a group and are filing this statement jointly pursuant to Rule 13d-1(k)(1) promulgated under the Exchange Act. (b) By virtue of the relationship previously reported under Item 2 of this statement, MS may be deemed to have shared voting and dispositive power with respect to the shares of Class A Common Stock owned by MS and MSIM. (c) During the past 60 days MSIM has effected the transactions in the Class A Common Stock set forth in Schedule C. (d) By virtue of the relationships described in Item 2 of this statement, MS may be deemed to have the power to direct the receipt of dividends declared on the shares of Class A Common stock held by MSIM and the proceeds from the sale of the shares of Class A Common Stock. (e) Not applicable. ------------------- ------------------ CUSIP NO. 650111107 13D PAGE 6 OF 15 PAGES ------------------- ------------------ Item 6. Contracts, Arrangements, Understandings or Relationships With Respect to Securities of the Issuer. ------ -------------------------------------------------------------- None. Item 7. Material to be Filed as Exhibits. ------ -------------------------------- Exhibit 2: Joint Filing Agreement* * Filed with original Schedule 13D ------------------- ------------------ CUSIP NO. 650111107 13D PAGE 7 OF 15 PAGES ------------------- ------------------ SIGNATURES 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. Dated: July 21, 2006 Morgan Stanley /s/ Dennine Bullard ----------------------------------------- By: Dennine Bullard Title: Authorized Signatory Morgan Stanley Investment Management Limited /s/ Jackie King ----------------------------------------- By: Jackie King Title: Authorized Signatory ------------------- ------------------ CUSIP NO. 650111107 13D PAGE 8 OF 15 PAGES ------------------- ------------------ SCHEDULE A EXECUTIVE OFFICERS AND DIRECTORS OF MORGAN STANLEY The names of the Directors and the names and titles of the Executive Officers of Morgan Stanley and their principal occupations are set forth below. The business address of each of the Directors or Executive Officers is that of Morgan Stanley at 1585 Broadway, New York, New York 10036. Unless otherwise indicated, each occupation set forth opposite an individual's name refers to Morgan Stanley and each individual is a United States citizen. Name, Business Address Present Principal Occupation ---------------------- ---------------------------- *Roy J. Bostock Chairman of the Partnership for a Drug Free America *Erskine B. Bowles President of the University of North Carolina *Sir Howard J. Davies(1) Director, London School of Economics and Political Science *C. Robert Kidder Principal, Stonehenge Partners, Inc. *John J. Mack Chairman of the Board and Chief Executive Officer *Donald T. Nicolaisen Director *Charles H. Noski Director *Hutham S. Olayan President and Chief Executive Officer of Olayan America Corporation and Director of the Olayan Group *Charles E. Phillips, Jr. President and Director of Oracle Corporation *O. Griffith Sexton Adjunct Professor of finance at Columbia Business School *Dr. Laura Andrea Tyson Dean of the London Business School *Dr. Klaus Zumwinkel(2) Chairman of the Board of Management, Deutsche Post AG Walid A. Chammah Head of Investment Banking Jonathan Chenevix-Trench(3) Chairman, Morgan Stanley International Zoe Cruz Co-President Thomas Daula Chief Risk Officer James P. Gorman President and COO, Global Wealth Management Group ---------------------- (1) Sir Howard Davies is a citizen of the United Kingdom (2) Klaus Zumwinkel is a German citizen (3) Jonathan Chenevix-Trench is a citizen of the United Kingdom ------------------- ------------------ CUSIP NO. 650111107 13D PAGE 9 OF 15 PAGES ------------------- ------------------ David Heleniak Vice Chairman Roger C. Hochschild President and COO, Discover Financial Services Jerker Johansson(4) Co-Head of Institutional Sales and Trading Gary G. Lynch Chief Legal Officer Alasdair Morrison(5) Chairman and CEO, Morgan Stanley Asia Eileen Murray Head of Global Operations and Technology David W. Nelms Chairman and CEO, Discover Financial Services Thomas Nides Chief Administrative Officer and Secretary Linda Riefler Chief Talent Officer Robert W. Scully Co-President Neal A. Shear Co-Head of Institutional Sales and Trading David H. Sidwell Executive Vice President and Chief Financial Officer Cordell G. Spencer(6) Deputy Head of Investment Banking Owen D. Thomas President and COO, Investment Management * Director ---------------------- (4) Jerker Johansson is a Swedish citizen (5) Alasdair Morrison is a citizen of the United Kingdom (6) Cordell Spencer is a Canadian citizen ------------------- ------------------- CUSIP NO. 650111107 13D PAGE 10 OF 15 PAGES ------------------- ------------------- SCHEDULE B EXECUTIVE OFFICERS AND DIRECTORS OF MORGAN STANLEY INVESTMENT MANAGEMENT LIMITED The names of the Directors and the names and titles of the Executive Officers of MSIM and their principal occupations are set forth below. The business address of each of the Directors or Executive Officers is that of MSIM at 25 Cabot Square, Canary Wharf, London E14 4QA, United Kingdom. Unless otherwise indicated, each occupation set forth opposite an individual's name refers to MSIM and each individual is a citizen of the United Kingdom. Name, Business Address Present Principal Occupation* ---------------------- ----------------------------- Michael S. Green Chief Executive Officer Hywel D. George Chief Investment Officer, London Equity Group J. David Germany Chief Investment Officer, Fixed Income Group Peter Wright Co-Head, International Equity Group Andrew Onslow Head of Operations **Hester Borrie Head of Sales * All of the individuals set forth above are Directors. ** Hester Borrie is a Dutch citizen. ------------------- ------------------- CUSIP NO. 650111107 13D PAGE 11 OF 15 PAGES ------------------- ------------------- SCHEDULE C MSIM has effected the following sales of Class A Common Stock during the past 60 days: DATE AMOUNT PRICE ---- ------- ----- 5/26/2006 94 $24.61 5/26/2006 153 $24.61 5/26/2006 387 $24.61 5/26/2006 2,245 $24.61 5/26/2006 409 $24.61 5/26/2006 814 $24.61 5/26/2006 1,035 $24.61 5/26/2006 34 $24.61 5/30/2006 269 $24.52 5/30/2006 3,059 $24.52 5/31/2006 238 $24.07 5/31/2006 174 $24.07 6/5/2006 226 $24.03 6/5/2006 127 $24.03 6/5/2006 112 $24.03 6/14/2006 1,938 $22.80 6/14/2006 280 $22.80 6/14/2006 79 $22.80 6/14/2006 36 $22.80 6/14/2006 127 $22.80 6/14/2006 62 $22.80 6/14/2006 2,741 $22.80 6/14/2006 309 $22.80 6/14/2006 1,326 $22.80 6/14/2006 397 $22.80 6/14/2006 635 $22.80 6/14/2006 204 $22.80 6/14/2006 668 $22.80 6/14/2006 77 $22.80 6/14/2006 18 $22.80 6/14/2006 7,411 $22.80 6/20/2006 145 $23.56 6/20/2006 259 $23.53 6/28/2006 2,789 $23.72 6/29/2006 346 $24.35 6/30/2006 1,515 $24.50 6/30/2006 624 $24.35 7/3/2006 319 $24.19 7/3/2006 1,861 $24.19 ------------------- ------------------- CUSIP NO. 650111107 13D PAGE 12 OF 15 PAGES ------------------- ------------------- 7/10/2006 1,627 $24.19 7/12/2006 33,982 $24.35 7/12/2006 39 $24.35 7/16/2006 1,921 $23.92 MSIM has effected the following purchases of Class A Common Stock during the past 60 days: DATE AMOUNT PRICE ---- ------- ----- 5/30/2006 496 $24.64 6/1/2006 31,976 $24.32 6/7/2006 6020 $24.11 6/5/2006 247 $24.10 6/13/2006 300 $23.30 6/14/2006 17,790 $22.80 6/19/2006 6,565 $23.77 6/19/2006 35 $23.77 6/21/2006 130,956 $24.26 6/21/2006 18,244 $24.25 6/22/2006 2,500 $24.31 6/22/2006 7,297 $24.44 6/22/2006 223,037 $24.34 6/23/2006 290,918 $23.91 6/23/2006 6,961 $24.03 6/26/2006 2,700 $23.88 6/26/2006 142,654 $23.79 6/27/2006 6,000 $23.79 6/27/2006 7,346 $23.87 6/27/2006 142,654 $23.76 6/28/2006 7,400 $23.77 6/28/2006 7,346 $23.71 6/29/2006 30,654 $23.91 6/29/2006 7,346 $23.87 6/29/2006 7,000 $23.90 6/29/2006 1,515 $24.50 7/5/2006 7,346 $24.00 7/5/2006 3,954 $24.00 7/6/2006 44 $24.41 7/13/2006 5,755 $23.99 7/13/2006 194,245 $23.96 7/14/2006 92,570 $23.82 7/15/2006 7,430 $23.82 7/17/2006 132,856 $23.50 7/17/2006 10,663 $23.49 ------------------- ------------------- CUSIP NO. 650111107 13D PAGE 13 OF 15 PAGES ------------------- ------------------- Other than the transactions described above, to the best of the Reporting Persons' knowledge, none of the executive officers and directors of the Reporting Persons (listed on attached Schedules A and B) nor any other Reporting Person have effected any transactions in the Class A Common Stock during the past 60 days. ------------------- ------------------- CUSIP NO. 650111107 13D PAGE 14 OF 15 PAGES ------------------- ------------------- EXHIBIT 1 Unless the context otherwise requires, the term "Morgan Stanley" means Morgan Stanley and its consolidated subsidiaries. (a) In April 2003, Morgan Stanley & Co. Incorporated ("MS&Co."), along with nine other financial services firms operating in the U.S., reached a settlement with the Securities and Exchange Commission ("SEC"), the New York State Attorney General's Office, the New York Stock Exchange ("NYSE"), the National Association of Securities Dealers, Inc. ("NASD"), and the North American Securities Administrators Association (on behalf of state securities regulators) to resolve their investigations relating to alleged research conflicts of interest. Without admitting or denying allegations with respect to violations of certain rules of the NYSE and NASD relating to investment research activities (there were no allegations of fraud or federal securities law violations made against MS&Co.), Morgan Stanley agreed, among other things, to (1) pay $25 million as a penalty, (2) pay $25 million as disgorgement of commissions and other monies, (3) provide $75 million over five years to make available independent third-party research to clients and (4) be permanently enjoined from violating certain rules of the NYSE and NASD relating to investment research activities. (b) In November 2003, Morgan Stanley DW Inc. ("MSDWI") consented, without admitting or denying the findings, to an entry of an order (the "Order") that resolved the SEC's and NASD's investigations into certain practices relating to MSDWI's offer and sale of certain mutual funds from January 1, 2000 to the date of the Order. Pursuant to the Order, MSDWI was ordered to (1) cease and desist from committing any violations and any future violations of Section 17(a)(2) of the Securities Act of 1933, as amended, and Rule 10b-10 under the Securities Exchange Act of 1934, as amended, (2) distribute for the benefit of certain customers who purchased funds through MSDWI pursuant to marketing arrangements between MSDWI and certain mutual fund complexes the amount of $50 million and (3) make certain disclosures and take certain other actions with respect to proprietary mutual funds. (c) In November 2004, Morgan Stanley reached a settlement with the SEC to resolve an informal accounting investigation by executing an offer of settlement and agreeing to entry of a cease-and-desist order. The SEC found that Morgan Stanley valued certain impaired aircraft in its aircraft leasing business in late 2001, late 2002 and early 2003, and certain bonds in its high-yield bond portfolio in late 2000, in a manner that did not comply with generally accepted accounting principles, and thus violated financial reporting, recordkeeping and internal control provisions of the federal securities laws. The resolution did not involve any restatement of past financial statements, any monetary penalty or any allegation of fraud. (d) In December 2004, MS&Co. and MSDWI reached a settlement with the NYSE under which Morgan Stanley executed two stipulations of facts and consent to penalty. The first stipulation was with respect to Morgan Stanley's failure to comply with certain prospectus delivery requirements, operational deficiencies and other matters, and ------------------- ------------------- CUSIP NO. 650111107 13D PAGE 15 OF 15 PAGES ------------------- ------------------- included a fine of $13 million. The second stipulation was with respect to employee defalcations, and included a fine of $6 million. (e) In January 2005, the SEC announced a settlement with MS&Co. and Goldman Sachs & Co. resolving the SEC's investigation relating to initial public offering ("IPO") allocation practices. The SEC filed a settled civil injunction action in the United States District Court for the District of Columbia against MS&Co. relating to the allocation of stock to institutional customers in IPOs underwritten during 1999 and 2000. Under the terms of the settlement, Morgan Stanley agreed, without admitting or denying the allegations, to the entry of a judgment enjoining it from violating Rule 101 of Regulation M and the payment of a $40 million civil penalty. The court approved the settlement on February 4, 2005. The complaint alleges that MS&Co. violated Rule 101 of Regulation M by attempting to induce certain customers who received allocations of IPOs to place purchase orders for additional shares in the aftermarket. (f) In May 2006, MS&Co. reached a settlement with the SEC, NYSE and NASD relating to its production of email in the research analyst and IPO investigations from December 2000 through at least July 2005. The complaint alleges that Morgan Stanley did not timely produce emails in response to requests in those matters because it did not diligently search for back-up tapes containing responsive emails until 2005, and because it over-wrote back-up tapes potentially containing responsive email until at least December 2002. Without admitting or denying the allegations of the complaint, Morgan Stanley consented to (1) a permanent injunction barring future violations of Section 17(b) of the Exchange Act (which requires, among other things, that Morgan Stanley respond promptly to SEC subpoenas and requests) and the relevant regulations promulgated thereunder and (2) the payment of a $15 million civil penalty, $5 million of which will be paid to NASD and the NYSE. In addition, MS&Co. and MSDWI have been involved in a number of civil proceedings which concern matters arising in connection with the conduct of its business. Certain of such proceedings have resulted in findings of violation of federal or state securities laws. Each of these proceedings was settled by MS&Co. and MSDWI consenting to the entry of an order without admitting or denying the allegations in the complaint. All of such proceedings are reported and summarized in the MS&Co. Form BD and the MSDWI Form BD filed with the SEC, which descriptions are hereby incorporated by reference.