Explanatory Note  

Introduction      

   This Final Amendment to Schedule 13D ("Final Amendment to Schedule 13D") amends Amendment No. 1 to Schedule 13D filed on July 27, 2007 ("Amendment No. 1 to Schedule 13D") by Millenco LLC, Millennium Management LLC and Israel A. Englander (the "Reporting Persons for Amendment No. 1 to Schedule 13D"), relating to their beneficial ownership of the Common Stock (as defined in Item 1, below), of Alexion Pharmaceuticals, Inc., a Delaware corporation (the "Issuer").

    This Final Amendment to Schedule 13D (i) amends and restates Items 1-7, (ii) reflects a material change in the number of shares beneficially owned by the Reporting Persons for Amendment No. 1 to Schedule 13D and the percentage of class represented by such ownership since the filing of the Amendment No. 1 to Schedule 13D for each of the Reporting Persons for Amendment No. 1 to Schedule 13D and (iii) adds Millennium Partners, L.P., Cognizant Holdings, Ltd., Integrated Holding Group LP, Millennium International Management LP and Millennium International Management GP LLC as Reporting Persons (as defined in Item 2, below). Except for the above-referenced amendments, this Final Amendment to Schedule 13D does not modify any of the information previously reported on Amendment No. 1 to Schedule 13D.

Item 1.      Security and Issuer.

    The name of the Issuer is Alexion Pharmaceuticals, Inc. The address of the Issuer’s principal executive offices is 352 Knotter Drive, Cheshire, Connecticut 06410. This Final Amendment to Schedule 13D relates to the Issuer’s common stock, par value $0.0001 per share (the "Common Stock"). Millenco LLC and Millennium Partners, L.P. also hold call options to purchase the Issuer’s Common Stock ("Options").

Item 2.      Identity and Background.

   (a)-(c), (f).  This statement is being filed by Millenco LLC, a Delaware limited liability company ("Millenco"), Millennium Partners, L.P., a Cayman Islands exempted limited partnership ("Millennium Partners") and Cognizant Holdings, Ltd., an exempted limited company organized under the laws of the Cayman Islands ("Cognizant Holdings"). Millenco is a broker-dealer and a member of the American Stock Exchange and the NASDAQ.

   Integrated Holding Group LP, a Delaware limited partnership ("Integrated Holding Group") is the 100% shareholder of Cognizant Holdings, and consequently may be deemed to have voting control and investment discretion over securities owned by Cognizant Holdings. Millennium Management LLC ("Millennium Management") is the manager of Millenco and the general partner of Millennium Partners and Integrated Holding Group, and consequently may be deemed to have voting control and investment discretion over securities owned by Millenco, Millennium Partners, Cognizant Holdings and securities deemed to be owned by Integrated Holding Group, as the case may be. Millennium International Management LP, a Delaware limited partnership ("Millennium International Management") is the investment manager to Cognizant Holdings, and consequently may be deemed to have voting control and investment discretion over securities owned by Cognizant Holdings. Millennium International Management GP LLC, a Delaware limited liability company ("Millennium International Management GP") is the general partner of Millennium International Management, and consequently may be deemed to have voting control and investment discretion over securities deemed to be beneficially owned by Millennium International Management. Israel A. Englander ("Mr. Englander") is the managing member of Millennium Management and of Millennium International Management GP, and consequently may be deemed to be the beneficial owner of any shares deemed to be beneficially owned by Millennium Management or Millennium International Management GP, as the case may be. The foregoing should not be construed in and of itself as an admission by Millennium Management, Integrated Holding Group, Millennium International Management, Millennium International Management GP, or Mr. Englander as to beneficial ownership of the shares owned by Millenco, Millennium Partners or Cognizant Holdings, as the case may be.

   Millenco, Millennium Partners, Cognizant Holdings, Integrated Holding Group, Millennium International Management, Millennium International Management GP, Millennium Management and Mr. Englander will be collectively referred to as the reporting persons ("Reporting Persons") in this Final Amendment to Schedule 13D.

   The business address for Millenco, Millennium Partners, Millennium Management, Integrated Holding Group and Mr. Englander is c/o Millennium Management LLC, 666 Fifth Avenue, New York, New York 10103. The business address for Cognizant Holdings, Millennium International Management, and Millennium International Management GP is c/o Millennium International Management LP, 666 Fifth Avenue, New York, New York 10103. Mr. Englander is a United States citizen.

   Note:  Integrated Holding Group is a non-managing member of Millenco. As a non-managing member, Integrated Holding Group has no voting control or investment discretion over Millenco or its securities positions.

   (d)  During the last five years, none of the Reporting Persons has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).

   (e)  On December 1, 2005, Millennium Management, Millennium International Management and Mr. Englander, together with Millennium Partners and certain related persons and entities, entered into settlements with the Securities and Exchange Commission ("SEC") and the Attorney General of the State of New York (the "NYAG") relating to allegations that Millennium Partners had engaged in a pattern of deceptive "market timing" of mutual fund shares in years prior to 2004 and, in the case of the settlement with the NYAG only, had failed to take adequate steps to prevent a trader from engaging in mutual fund "late trading" in violation of firm policy. The parties neither admitted nor denied the allegations or findings (except as to jurisdiction) but consented to the entry of findings. The SEC proceedings are In the Matter of Millennium Partners, L.P., et al. Securities Act Release No. 8639 (December 1, 2005), available at www.sec.gov. Contemporaneously, the NYAG issued an Assurance of Discontinuance relating to the claims and findings of that office.

    Neither the Reporting Persons nor any other party admitted or denied any of the allegations or findings in these matters. The remedies included disgorgement by the entities of approximately $148 million of mutual fund trading profits, civil penalties aggregating approximately $32.15 million (with approximately $30 million being paid by Mr. Englander), an administrative order to cease and desist from violations of the antifraud provisions of the Securities Act of 1933 and the Securities Exchange Act of 1934 (the "Exchange Act"), and prophylactic relief.

Item 3.      Source and Amount of Funds or Other Consideration.

   The amount of funds used to purchase the 1,441,296, 500,000 and 2,114 shares of the Issuer’s Common Stock beneficially owned by Millenco, Millennium Partners and Cognizant Holdings, respectively, in the transactions giving rise to this Final Amendment to Schedule 13D was approximately $40,128,877, $8,482,500 and $150,668, respectively, calculated on an average cost basis (excluding brokerage commissions) by account. Millenco, Millennium Partners and Cognizant Holdings effect purchases of securities primarily through margin accounts maintained for Millenco, Millennium Partners and Cognizant Holdings with prime brokers, which may extend margin credit to Millenco, Millennium Partners and Cognizant Holdings as and when required to open or carry positions in the margin accounts, subject to applicable margin regulations, stock exchange rules and the prime broker’s credit policies. In such instances, the positions held in the margin accounts are pledged as collateral security for the repayment of debit balances in the accounts.

Item 4.       Purpose of Transaction.

   The Reporting Persons are engaged in the investment business. In pursuing this business, the Reporting Persons analyze the operations, capital structure and markets of companies, including the Issuer, on a continuous basis through analysis of documentation and discussions with knowledgeable industry and market observers and with representatives of such companies (often at the invitation of management). From time to time, one or more of the Reporting Persons may hold discussions with third parties or with management of such companies in which the Reporting Persons may suggest or take a position with respect to potential changes in the operations, management or capital structure of such companies as a means of enhancing shareholder value. Such suggestions or positions may relate to one or more of the transactions specified in clauses (a) through (j) of Item 4 of Schedule 13D of the Exchange Act, including, without limitation, such matters as disposing of or selling all or a portion of the company or acquiring another company or business, changing operating or marketing strategies, adopting or not adopting certain types of anti-takeover measures and restructuring the Issuer’s capitalization or dividend policy.

   The Reporting Persons employ the services of a number of portfolio managers, each of whom independently employs a separate and distinct trading strategy. A portion of the securities of the Issuer held by the Reporting Persons are held in accounts of the Reporting Persons managed by portfolio managers who engage in event-, risk- or merger-arbitrage or fundamental strategies.

   Except as set forth above, the Reporting Persons do not have any present plans or proposals that relate to or would result in any of the actions required to be described in Item 4 of Schedule 13D. Each of the Reporting Persons may, at any time, review or reconsider its position with respect to the Issuer and formulate plans or proposals with respect to any of such matters, but has no present intention of doing so.

Item 5.      Interest in Securities of the Issuer.

   (a)  As of the date hereof: (i) Millenco is the beneficial owner of 1,441,296 shares of the Issuer’s Common Stock (consisting of 691,296 shares of the Issuer’s Common Stock and Options to purchase an aggregate of 750,000 shares of the Issuer’s Common Stock); (ii) Millennium Partners is the beneficial owner of 500,000 shares of the Issuer’s Common Stock (by virtue of holding an Option to purchase 500,000 shares of the Issuer’s Common Stock); and (iii) Cognizant Holdings is the beneficial owner of 2,114 shares of the Issuer’s Common Stock.

   Integrated Holding Group, as the 100% shareholder of Cognizant Holdings, may also be deemed to beneficially own the above-described shares of the Issuer’s Common Stock beneficially owned by Cognizant Holdings.

   Millennium Management, as the manager of Millenco and the general partner of Millennium Partners and Integrated Holding Group, may also be deemed to beneficially own the above-described shares of the Issuer’s Common Stock beneficially owned by Millenco, Millennium Partners or Cognizant Holdings, as the case may be.

   Millennium International Management GP, as the general partner of Millennium International Management, may also be deemed to beneficially own the above-described shares of the Issuer’s Common Stock beneficially owned by Cognizant Holdings.

   Mr. Englander, as the managing member of Millennium Management and of Millennium International Management GP, may also be deemed to beneficially own the above-described shares of the Issuer’s Common Stock beneficially owned by Millenco, Millennium Partners or Cognizant Holdings, as the case may be.

   Accordingly, as of the date of this filing, Millennium Management and Mr. Englander may be deemed to be beneficial owners of 1,943,410 shares of the Issuer’s Common Stock which represents approximately 4.9% of the outstanding Common Stock. The calculation of the foregoing percentage is on the basis of 38,182,368 shares of the Issuer’s Common Stock outstanding as of March 24, 2008, as disclosed in the Issuer’s Proxy Statement, dated April 4, 2008. Integrated Holding Group, Millennium International Management and Millennium International Management GP may be deemed to be the beneficial owners of 2,114 shares of the Issuer’s Common Stock.

   The foregoing should not be construed in and of itself as an admission by Millennium Management, Integrated Holding Group, Millennium International Management, Millennium International Management GP or Mr. Englander as to beneficial ownership of the shares held by Millenco, Millennium Partners or Cognizant Holdings, as the case may be.

   (b)  Millenco may be deemed to hold shared power to vote and to dispose of the 1,441,296 shares of the Issuer’s Common Stock described in (a) above. Millennium Partners may be deemed to hold shared power to vote and to dispose of the 500,000 shares of the Issuer’s Common Stock described in (a) above. Cognizant Holdings, Integrated Holding Group, Millennium International Management, and Millennium International Management GP may be deemed to hold shared power to vote and to dispose of the 2,114 shares of the Issuer’s Common Stock described in (a) above. Mr. Englander and Millennium Management may be deemed to hold shared power to vote and to dispose of the 1,943,410 shares of the Issuer’s Common Stock described in (a) above. The foregoing should not be construed in and of itself as an admission by Mr. Englander, Millennium Management, Integrated Holding Group, Millennium International Management or Millennium International Management GP as to beneficial ownership of the shares held by Millenco, Millennium Partners or Cognizant Holdings, as the case may be.

   (c)  Transactions in the Issuer’s Common Stock during the past 60 days: Schedule A annexed hereto lists all transactions in the Issuer’s Common Stock during the past 60 days by the Reporting Persons. All transactions during the past 60 days were effected by either Millenco or Cognizant Holdings in the open market.

   (d)  No person other than the Reporting Persons is known to have the right to receive, or the power to direct the receipt of, dividends from, or proceeds from the sale of, the shares of Common Stock reported in this Statement.

   (e)  On May 7, 2008, the Reporting Persons ceased to beneficially own in excess of 5% of the Issuer’s Common Stock.

Item 6.      Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer.

   Millenco maintains an open short position of 300,982 shares of the Issuer’s Common Stock, which position is not netted against the data provided herein as to the number of shares beneficially owned by the Reporting Persons.

   In connection with arrangements with Millenco’s, Millennium Partners’s and Cognizant Holdings’s prime brokers, such prime brokers are permitted to lend securities in Millenco’s, Millennium Partners’s and Cognizant Holdings’s accounts (as the case may be) to the extent permitted by debit balances in such accounts. Millenco, Millennium Partners and Cognizant Holdings generally will not have any knowledge of the specific loans made by such prime brokers. In addition, in the ordinary course of business, Millenco, Millennium Partners and Cognizant Holdings (or their prime brokers), may borrow securities to satisfy delivery obligations arising from short sales and may lend securities to third parties and such loans generally may be recalled upon demand. However, it should be noted that shares lent by Millenco, Millennium Partners, Cognizant Holdings or their prime brokers may not be able to be recalled in advance of an applicable record date and thus, such loaned shares may not be able to be voted by Millenco, Millennium Partners and Cognizant Holdings (as the case may be). As of the date hereof, Millenco has lent 20,300 shares of the Issuer’s Common Stock to third parties.

   There are no other contracts, arrangements, understandings or relationships among the Reporting Persons, or between the Reporting Persons and any other person, with respect to the securities of the Issuer.

Item 7.      Material to Be Filed as Exhibits.

   Exhibit I:  Joint Filing Agreement, dated as of May 7, 2008, by and among Millenco LLC, Millennium Partners, L.P., Cognizant Holdings, Ltd., Integrated Holding Group LP, Millennium International Management LP, Millennium International Management GP LLC, Millennium Management LLC and Israel A. Englander.

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.

Dated: May 7, 2008