UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D Under the Securities Act of 1934 (Amendment No. 1) BROOKS AUTOMATION, INC. (BRKS) (Name of Issuer) Common Stock (Title of Class of Securities) 114340102 (CUSIP Number) David Nierenberg The D3 Family Funds 19605 NE 8th Street Camas, WA 98607 360-604-8600 ------------------------------------------------------------- (Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications) July 15, 2005 (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 ss.ss.240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box: |_| -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON The D3 Family Fund, L.P. (David Nierenberg is president of the General Partner, which is Nierenberg Investment Management Company.) -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |X| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 SOURCE OF FUNDS* WC -------------------------------------------------------------------------------- 5 CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e) |_| -------------------------------------------------------------------------------- 6 CITIZENSHIP OR PLACE OF ORGANIZATION USA -------------------------------------------------------------------------------- 7 SOLE VOTING POWER 1,269,556 common shares (2.8%) ----------------------------------------------------------------- NUMBER OF 8 SHARED VOTING POWER SHARES BENEFICIALLY 0 OWNED BY ----------------------------------------------------------------- EACH 9 SOLE DISPOSITIVE POWER REPORTING PERSON 1,269,556 WITH ----------------------------------------------------------------- 10 SHARED DISPOSITIVE POWER 0 -------------------------------------------------------------------------------- 11 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 2,571,156 shares (5.7%) -------------------------------------------------------------------------------- 12 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 13 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 5.7% -------------------------------------------------------------------------------- 14 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! 2 -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON The D3 Family Retirement Fund, L.P. (David Nierenberg is president of the General Partner, which is Nierenberg Investment Management Company.) -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |X| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 SOURCE OF FUNDS* WC -------------------------------------------------------------------------------- 5 CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e) |_| -------------------------------------------------------------------------------- 6 CITIZENSHIP OR PLACE OF ORGANIZATION USA -------------------------------------------------------------------------------- 7 SOLE VOTING POWER 394,700 common shares (0.87%) ----------------------------------------------------------------- NUMBER OF 8 SHARED VOTING POWER SHARES BENEFICIALLY 0 OWNED BY ----------------------------------------------------------------- EACH 9 SOLE DISPOSITIVE POWER REPORTING PERSON 394,700 WITH ----------------------------------------------------------------- 10 SHARED DISPOSITIVE POWER 0 -------------------------------------------------------------------------------- 11 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 2,571,156 shares (5.7%) -------------------------------------------------------------------------------- 12 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 13 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 5.7% -------------------------------------------------------------------------------- 14 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! 3 -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON The D3 Children's Fund, L.P. (David Nierenberg is president of the General Partner, which is Nierenberg Investment Management Company.) -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |X| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 SOURCE OF FUNDS* WC -------------------------------------------------------------------------------- 5 CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e) |_| -------------------------------------------------------------------------------- 6 CITIZENSHIP OR PLACE OF ORGANIZATION USA -------------------------------------------------------------------------------- 7 SOLE VOTING POWER 94,900 common shares (0.21%) ----------------------------------------------------------------- NUMBER OF 8 SHARED VOTING POWER SHARES BENEFICIALLY 0 OWNED BY ----------------------------------------------------------------- EACH 9 SOLE DISPOSITIVE POWER REPORTING PERSON 94,900 WITH ----------------------------------------------------------------- 10 SHARED DISPOSITIVE POWER 0 -------------------------------------------------------------------------------- 11 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 2,571,156 shares (5.7%) -------------------------------------------------------------------------------- 12 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 13 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 5.7% -------------------------------------------------------------------------------- 14 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! 4 -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON The D3 Offshore Fund, L.P. (David Nierenberg is president of the General Partner, which is Nierenberg Investment Management Company.) -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |X| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 SOURCE OF FUNDS* WC -------------------------------------------------------------------------------- 5 CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e) |_| -------------------------------------------------------------------------------- 6 CITIZENSHIP OR PLACE OF ORGANIZATION USA -------------------------------------------------------------------------------- 7 SOLE VOTING POWER 617,650 common shares (1.36%) ----------------------------------------------------------------- NUMBER OF 8 SHARED VOTING POWER SHARES BENEFICIALLY 0 OWNED BY ----------------------------------------------------------------- EACH 9 SOLE DISPOSITIVE POWER REPORTING PERSON 617,650 WITH ----------------------------------------------------------------- 10 SHARED DISPOSITIVE POWER 0 -------------------------------------------------------------------------------- 11 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 2,571,156 shares (5.7%) -------------------------------------------------------------------------------- 12 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 13 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 5.7% -------------------------------------------------------------------------------- 14 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! 5 -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON The D3 Family Bulldog Fund, L.P. (David Nierenberg is president of the General Partner, which is Nierenberg Investment Management Company.) -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |X| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 SOURCE OF FUNDS* WC -------------------------------------------------------------------------------- 5 CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e) |_| -------------------------------------------------------------------------------- 6 CITIZENSHIP OR PLACE OF ORGANIZATION USA -------------------------------------------------------------------------------- 7 SOLE VOTING POWER 194,350 common shares (0.43%) ----------------------------------------------------------------- NUMBER OF 8 SHARED VOTING POWER SHARES BENEFICIALLY 0 OWNED BY ----------------------------------------------------------------- EACH 9 SOLE DISPOSITIVE POWER REPORTING PERSON 194,350 WITH ----------------------------------------------------------------- 10 SHARED DISPOSITIVE POWER 0 -------------------------------------------------------------------------------- 11 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 2,571,156 shares (5.7%) -------------------------------------------------------------------------------- 12 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 13 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 5.7% -------------------------------------------------------------------------------- 14 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! 6 Item 1. Security and Issuer. Common stock in BROOKS AUTOMATION, INC. (BRKS) 15 Elizabeth Drive, Chelmsford, MA 01824-4111. Item 2. Identity and Background. The D3 Family Fund, L.P. is a Washington State limited partnership, whose principal business is investing in the equities of public micro-cap issuers. Located at 19605 N.E. 8th St., Camas, Washington 98607. No convictions or administrative proceedings as described in 2 (d) and (e). Item 3. Source and Amount of Funds or Other Consideration Source of funds is money invested in the partnership by its partners. Item 4. Purpose of Transaction Because we enthusiastically support BRKS acquisition of HELX, we acquired additional shares of BRKS. Not only has BRKS characterized the financial impact of this acquisition as "significantly accretive" (language which has real meaning at a time when lawyers agonize over every word in a press release), we also believe the acquisition will bring several important strategic and operating benefits to the combined company: o The combined companies will control 51% and potentially up to 66% of the value added content of the vacuum robotic systems they will manufacture, a large enough share of the value added to enable them to offer meaningful savings to Tier 1 semi-conductor capital equipment OEM's who are considering outsourcing their vacuum robotics systems to BRKS. We believe this acquisition will create a company with enough capability and scale to accelerate this outsourcing process. o HELX's field service capabilities will enable BRKS to more rapidly grow this profitable, stable source of recurring revenue. o We believe the overall management of the combined company will be strengthened through the merger, with BRKS bringing strong financial management and HELX strong operating and global manufacturing management. o Because the combined company will be one of the largest semiconductor capital equipment subsystems suppliers, we hope shareholders might enjoy greater liquidity and higher valuations. 7 o Finally, we observed at Semicon West this week that the two CEO's of the companies already work very well together. We think the risk of friction is exceptionally low, both because the business lines are complementary and because of the flexible, accommodating personalities of the two CEO's. Item 5. Interest in Securities of the Issuer. (a,b) The D3 Family Fund, L.P. owns and has sole voting and dispositive power over 1,269,556 common shares of BRKS. (c) Date Shares Bought Price ------- ------------- ----- 7/11/05 90,300 14.66 7/14/05 123,700 15.39 (d) N/A (e) N/A Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer. N/A Item 7. Material to be Filed as Exhibits N/A SIGNATURE After reasonable inquiry and to the best of my knowledge and belief, each of the undersigned certifies that the information set forth in the Statement is true, complete and correct. July 15, 2005 /s/ DAVID NIERENBERG ---------------------------------------- David Nierenberg President Nierenberg Investment Management Company, Inc., the General Partner of The D3 Family Fund, L.P 8 Item 1. Security and Issuer. Common stock in BROOKS AUTOMATION, INC. (BRKS) 15 Elizabeth Drive, Chelmsford, MA 01824-4111. Item 2. Identity and Background. The D3 Family Retirement Fund, L.P. is a Washington State limited partnership, whose principal Business is investing in the equities of public micro-cap issuers. Located at 19605 N.E. 8th St., Camas, Washington 98607. No convictions or administrative proceedings as described in 2 (d) and (e). Item 3. Source and Amount of Funds or Other Consideration Source of funds is money invested in the partnership by its partners. Item 4. Purpose of Transaction Because we enthusiastically support BRKS acquisition of HELX, we acquired additional shares of BRKS. Not only has BRKS characterized the financial impact of this acquisition as "significantly accretive" (language which has real meaning at a time when lawyers agonize over every word in a press release), we also believe the acquisition will bring several important strategic and operating benefits to the combined company: o The combined companies will control 51% and potentially up to 66% of the value added content of the vacuum robotic systems they will manufacture, a large enough share of the value added to enable them to offer meaningful savings to Tier 1 semi-conductor capital equipment OEM's who are considering outsourcing their vacuum robotics systems to BRKS. We believe this acquisition will create a company with enough capability and scale to accelerate this outsourcing process. o HELX's field service capabilities will enable BRKS to more rapidly grow this profitable, stable source of recurring revenue. o We believe the overall management of the combined company will be strengthened through the merger, with BRKS bringing strong financial management and HELX strong operating and global manufacturing management. o Because the combined company will be one of the largest semiconductor capital equipment subsystems suppliers, we hope shareholders might enjoy greater liquidity and higher valuations. 9 o Finally, we observed at Semicon West this week that the two CEO's of the companies already work very well together. We think the risk of friction is exceptionally low, both because the business lines are complementary and because of the flexible, accommodating personalities of the two CEO's. Item 5. Interest in Securities of the Issuer. (a,b) The D3 Family Retirement Fund, L.P. owns and has sole voting and dispositive power over 394,700 common shares of BRKS. (c) Date Shares Bought Price ------- ------------- ----- 7/11/05 21,900 14.66 7/14/05 39,300 15.39 (d) N/A (e) N/A Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer. N/A Item 7. Material to be Filed as Exhibits N/A 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. July 15, 2005 /s/ DAVID NIERENBERG Date ------------------------------------------ David Nierenberg President Nierenberg Investment Management Company, Inc., the General Partner of the D3 Family Retirement Fund, L.P. 10 Item 1. Security and Issuer. Common stock in BROOKS AUTOMATION, INC. (BRKS) 15 Elizabeth Drive, Chelmsford, MA 01824-4111. Item 2. Identity and Background. The D3 Children's Fund, L.P. is a Washington State limited partnership, whose principal business is investing in the equities of public micro-cap Issuers. Located at 19605 N.E. 8th St., Camas,Washington 98607. No convictions or administrative proceedings as described in 2 (d) and (e). Item 3. Source and Amount of Funds or Other Consideration Source of funds is money invested in the partnership by its partners. Item 4. Purpose of Transaction Because we enthusiastically support BRKS acquisition of HELX, we acquired additional shares of BRKS. Not only has BRKS characterized the financial impact of this acquisition as "significantly accretive" (language which has real meaning at a time when lawyers agonize over every word in a press release), we also believe the acquisition will bring several important strategic and operating benefits to the combined company: o The combined companies will control 51% and potentially up to 66% of the value added content of the vacuum robotic systems they will manufacture, a large enough share of the value added to enable them to offer meaningful savings to Tier 1 semi-conductor capital equipment OEM's who are considering outsourcing their vacuum robotics systems to BRKS. We believe this acquisition will create a company with enough capability and scale to accelerate this outsourcing process. o HELX's field service capabilities will enable BRKS to more rapidly grow this profitable, stable source of recurring revenue. o We believe the overall management of the combined company will be strengthened through the merger, with BRKS bringing strong financial management and HELX strong operating and global manufacturing management. o Because the combined company will be one of the largest semiconductor capital equipment subsystems suppliers, we hope shareholders might enjoy greater liquidity and higher valuations. o Finally, we observed at Semicon West this week that the two CEO's of the companies already work very well together. We think the risk of 11 friction is exceptionally low, both because the business lines are complementary and because of the flexible, accommodating personalities of the two CEO's. Item 5. Interest in Securities of the Issuer. (a,b) The D3 Children's Fund, L.P. owns and has sole voting and dispositive power over 94,900 common shares of BRKS. (c) Date Shares Bought Price ------- ------------- ----- 6/15/05 1,000 15.64 7/11/05 14,000 14.66 7/14/05 9,500 15.39 (d) N/A (e) N/A Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer. N/A Item 7. Material to be Filed as Exhibits N/A SIGNATURE After reasonable inquiry and to the best of my knowledge and belief, each of the undersigned certifies that the information set forth in the Statement is true, complete and correct. July 15, 2005 /s/ DAVID NIERENBERG ------------------------------------------ David Nierenberg President Nierenberg Investment Management Company, Inc., the General Partner of The D3 Children's Fund, L.P. 12 Item 1. Security and Issuer. Common stock in BROOKS AUTOMATION, INC. (BRKS) 15 Elizabeth Drive, Chelmsford, MA 01824-4111. Item 2. Identity and Background. The D3 Offshore Fund, L.P. is a Washington State limited partnership, whose principal business is investing in the equities of public micro-cap issuers. Located at 19605 N.E. 8th St., Camas, Washington 98607. No convictions or administrative proceedings as described in 2 (d) and (e). Item 3. Source and Amount of Funds or Other Consideration Source of funds is money invested in the partnership by its partners. Item 4. Purpose of Transaction Because we enthusiastically support BRKS acquisition of HELX, we acquired additional shares of BRKS. Not only has BRKS characterized the financial impact of this acquisition as "significantly accretive" (language which has real meaning at a time when lawyers agonize over every word in a press release), we also believe the acquisition will bring several important strategic and operating benefits to the combined company: o The combined companies will control 51% and potentially up to 66% of the value added content of the vacuum robotic systems they will manufacture, a large enough share of the value added to enable them to offer meaningful savings to Tier 1 semi-conductor capital equipment OEM's who are considering outsourcing their vacuum robotics systems to BRKS. We believe this acquisition will create a company with enough capability and scale to accelerate this outsourcing process. o HELX's field service capabilities will enable BRKS to more rapidly grow this profitable, stable source of recurring revenue. o We believe the overall management of the combined company will be strengthened through the merger, with BRKS bringing strong financial management and HELX strong operating and global manufacturing management. o Because the combined company will be one of the largest semiconductor capital equipment subsystems suppliers, we hope shareholders might enjoy greater liquidity and higher valuations. o Finally, we observed at Semicon West this week that the two CEO's of the companies already work very well together. We think the risk of 13 friction is exceptionally low, both because the business lines are complementary and because of the flexible, accommodating personalities of the two CEO's. Item 5. Interest in Securities of the Issuer. (a,b) The D3 Offshore Fund, L.P. owns and has sole voting and dispositive power over 617,650 common shares of BRKS. (c) Date Shares Bought Price ------- ------------- ----- 5/18/05 40,000 14.29 5/23/05 30,000 14.42 5/24/05 5,700 14.38 5/25/05 7,000 14.28 6/1/05 10,000 15.38 6/2/05 10,000 15.62 6/3/05 25,000 15.29 6/6/05 43,500 15.05 6/7/05 20,000 15.22 6/8/05 15,000 15.29 6/9/05 5,000 15.36 6/13/05 10,000 15.73 6/14/05 22,000 15.74 6/15/05 4,400 15.62 6/24/05 10,000 15.33 7/11/05 102,300 14.66 7/14/05 58,750 15.39 (d) N/A (e) N/A Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer. N/A Item 7. Material to be Filed as Exhibits N/A SIGNATURE After reasonable inquiry and to the best of my knowledge and belief, each of the undersigned certifies that the information set forth in the Statement is true, complete and correct. July 15, 2005 /s/ DAVID NIERENBERG -------------------- David Nierenberg President Nierenberg Investment Management Company, Inc., the General Partner of the D3 Offshore Fund, L.P. 14 Item 1. Security and Issuer. Common stock in BROOKS AUTOMATION, INC. (BRKS) 15 Elizabeth Drive, Chelmsford, MA 01824-4111. Item 2. Identity and Background. The D3 Family Bulldog Fund, L.P. is a Washington State limited partnership, whose principal business is investing in the equities of public micro-cap issuers. Located at 19605 N.E. 8th St., Camas,Washington 98607. No convictions or administrative proceedings as described in 2 (d) and (e). Item 3. Source and Amount of Funds or Other Consideration Source of funds is money invested in the partnership by its partners. Item 4. Purpose of Transaction Because we enthusiastically support BRKS acquisition of HELX, we acquired additional shares of BRKS. Not only has BRKS characterized the financial impact of this acquisition as "significantly accretive" (language which has real meaning at a time when lawyers agonize over every word in a press release), we also believe the acquisition will bring several important strategic and operating benefits to the combined company: o The combined companies will control 51% and potentially up to 66% of the value added content of the vacuum robotic systems they will manufacture, a large enough share of the value added to enable them to offer meaningful savings to Tier 1 semi-conductor capital equipment OEM's who are considering outsourcing their vacuum robotics systems to BRKS. We believe this acquisition will create a company with enough capability and scale to accelerate this outsourcing process. o HELX's field service capabilities will enable BRKS to more rapidly grow this profitable, stable source of recurring revenue. o We believe the overall management of the combined company will be strengthened through the merger, with BRKS bringing strong financial management and HELX strong operating and global manufacturing management. o Because the combined company will be one of the largest semiconductor capital equipment subsystems suppliers, we hope shareholders might enjoy greater liquidity and higher valuations. 15 o Finally, we observed at Semicon West this week that the two CEO's of the companies already work very well together. We think the risk of friction is exceptionally low, both because the business lines are complementary and because of the flexible, accommodating personalities of the two CEO's. Item 5. Interest in Securities of the Issuer. (a,b) The D3 Family Bulldog Fund, L.P. owns and has sole voting and dispositive power over 194,350 common shares of BRKS. (c) Date Shares Bought Price ------- ------------- ----- 6/14/05 18,000 15.74 7/11/05 20,800 14.66 7/14/05 18,750 15.39 (d) N/A (e) N/A Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer. N/A Item 7. Material to be Filed as Exhibits N/A SIGNATURE After reasonable inquiry and to the best of my knowledge and belief, each of the undersigned certifies that the information set forth in the Statement is true, complete and correct. July 15, 2005 /s/ DAVID NIERENBERG ------------------------------------------ David Nierenberg President Nierenberg Investment Management Company, Inc., the General Partner of The D3 Family Bulldog Fund, L.P. 16