13D Filing: MHR Fund Management and Emisphere Technologies Inc (EMIS)

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SECURITIES AND EXCHANGE
COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Rule 13d-101

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO
§ 240.13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO § 240.13d-2(a)

(Amendment No. 28)*

(Name of Issuer)

(Title of Class of Securities)

(CUSIP Number)

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

(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
§§240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box  ☐.

Note: Schedules filed in paper format
shall include a signed original and five copies of the schedule, including all exhibits. See §240.13d-7 for other parties to whom copies are to be sent.

The information
required on the remainder of this cover page shall not be deemed to be filed for the purpose of Section 18 of the Securities Exchange Act of 1934 (Act) or otherwise subject to the liabilities of that section of
the Act but shall be subject to all other provisions of the Act (however, see the Notes).

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This statement on Schedule 13D (this Statement) further amends and supplements, as
Amendment No. 28, the Schedule 13D filed on October 6, 2005 (the Initial 13D), as amended by Amendment No. 1, filed on January 18, 2006 (Amendment No. 1), Amendment No. 2,
filed on May 11, 2006 (Amendment No. 2), Amendment No. 3, filed on August 20, 2007 (Amendment No. 3), Amendment No. 4, filed on August 24, 2007 (Amendment
No. 4), Amendment No. 5, filed on July 2, 2008 (Amendment No. 5), Amendment No. 6, filed on July 2, 2009 (Amendment No. 6), Amendment No. 7, filed on
August 21, 2009 (Amendment No. 7), Amendment No. 8, filed on August 25, 2009 (Amendment No. 8), Amendment No. 9, filed on June 9, 2010 (Amendment
No. 9), Amendment No. 10, filed on August 2, 2010 (Amendment No. 10), Amendment No. 11, filed on August 27, 2010 (Amendment No. 11), Amendment No. 12, filed on
December 22, 2010 (Amendment No. 12), Amendment No. 13, filed on July 1, 2011 (Amendment No. 13), Amendment No. 14, filed on July 8, 2011 (Amendment
No. 14), Amendment No. 15, filed on June 5, 2012 (Amendment No. 15), Amendment No. 16, filed on September 27, 2012 (Amendment No. 16), Amendment No. 17, filed on
October 9, 2012 (Amendment No. 17), Amendment No. 18, filed on October 19, 2012 (Amendment No. 18), Amendment No. 19, filed on January 10, 2013
(Amendment 19), Amendment No. 20, filed on April 30, 2013 (Amendment No. 20), Amendment No. 21, filed on May 9, 2013 (Amendment No. 21), Amendment No. 22,
filed on March 31, 2014 (Amendment No. 22), Amendment No. 23, filed on August 22, 2014 (Amendment No. 23), Amendment No. 24, filed on July 1, 2015 (Amendment No. 24),
Amendment No. 25, filed on October 15, 2015 (Amendment No. 25), Amendment No. 26, filed on July 5, 2016 (Amendment No. 26) and Amendment No. 27, filed on December 9, 2016
(Amendment No. 27, and, together with the Initial 13D and Amendment No. 1 through Amendment No. 26, the Schedule 13D) and relates to shares of common stock, par value $0.01 per share
(the Shares), of Emisphere Technologies, Inc. (the Issuer). Except as otherwise provided, defined terms used in this Statement but not defined herein shall have the respective meanings given such terms in
Amendment No. 27.

Item 5 is hereby amended by deleting such item in its entirety and replacing it with the following:

The percentages set forth in this Statement are calculated based on information contained in the Issuers Form 10-Q for the quarterly period ended March 31, 2017, which disclosed that there
were 60,852,478 Shares outstanding as of May 1, 2017.

All percentages of beneficial ownership presented herein are
calculated after giving effect to the issuance of the Shares pursuant to exercise or vesting of warrants, restricted stock or stock options currently owned by the Reporting Persons, and assuming such Reporting Persons Convertible Notes, Bridge
Notes and Reimbursement Notes were converted into Shares as of such date.

(a) (i) Master Account may be deemed the
beneficial owner of 22,544,146 Shares (approximately 29.2% of the total number of Shares outstanding, calculated in accordance with Rule 13d-3(d)(1)(i) under the Act). This number consists of (A) 6,226,054 Shares held for the account of Master
Account, (B) 5,515,644 Shares that can be obtained by Master Account upon exercise of warrants to acquire Shares, (C) 9,102,402 Shares that can be obtained by Master Account upon the conversion of the Convertible Notes, (D) 1,346,800
Shares that can be obtained by Master Account upon the conversion of the Bridge Notes and (E) 353,246 Shares that can be obtained by Master Account upon the conversion of the Reimbursement Notes.

(ii) Capital Partners (100) may be deemed the beneficial owner of 3,036,294 Shares (approximately 4.8% of the total number of Shares
outstanding, calculated in accordance with Rule 13d-3(d)(1)(i) under the Act). This number consists of (A) 847,125 Shares held for the account of Capital Partners (100), (B) 716,030 Shares that can be obtained by Capital Partners
(100) upon exercise of warrants to acquire Shares, (C) 1,244,771 Shares that can be obtained by Capital Partners (100) upon the conversion of the Convertible Notes, (D) 179,156 Shares that can be obtained by Capital Partners
(100) upon the conversion of the Bridge Notes and (E) 49,212 Shares that can be obtained by Capital Partners (100) upon the conversion of the Reimbursement Notes.

(iii) Advisors may be deemed the beneficial owner of 25,580,440 Shares (approximately 32.2% of the total number of Shares outstanding,
calculated in accordance with Rule 13d-3(d)(1)(i) under the Act). This number consists of (A) (1) 6,226,054 Shares held for the account of Master Account, (2) 5,515,644 Shares that can be obtained by Master Account upon exercise of
warrants to acquire Shares, (3) 9,102,402 Shares that can be obtained by Master Account upon the conversion of the Convertible Notes, (4) 1,346,800 Shares that can be obtained by Master Account upon the conversion of the Bridge Notes and
(5) 353,246 Shares that can be obtained by Master Account upon the conversion of the Reimbursement Notes, and (B) (1) 847,125 Shares held for the account of Capital Partners (100), (2) 716,030 Shares that can be obtained by
Capital Partners (100) upon exercise of warrants to acquire Shares, (3) 1,244,771 Shares that can be obtained by Capital Partners (100) upon the conversion of Convertible Notes, (4) 179,156 Shares that can be obtained by Capital
Partners (100) upon the conversion of Bridge Notes and (5) 49,212 Shares that can be obtained by Capital Partners (100) upon the conversion of Reimbursement Notes.

(iv) Institutional Partners II may be deemed the beneficial owner of 19,038,877 Shares (approximately 24.8% of the total number of Shares
outstanding, calculated in accordance with Rule 13d-3(d)(1)(i) under the Act). This number consists of (A) 3,240,750 Shares held for the account of Institutional Partners II, (B) 4,479,892 Shares that can be obtained by Institutional
Partners II upon the exercise of warrants to acquire Shares, (C) 9,904,157 Shares that can be obtained by Institutional Partners II upon the conversion of the Convertible Notes, (D) 1,029,196 Shares that can be obtained by Institutional
Partners II upon the conversion of the Bridge Notes and (E) 384,882 Shares that can be obtained by Institutional Partners II upon the conversion of the Reimbursement Notes.

(v) Institutional Partners IIA may be deemed the beneficial owner of 47,965,212 Shares (approximately 47.7% of the total number of Shares
outstanding, calculated in accordance with Rule 13d-3(d)(1)(i) under the Act). This number consists of (A) 8,164,436 Shares held for the account of Institutional Partners IIA, (B) 11,286,210 Shares that can be obtained by Institutional
Partners IIA upon the exercise of warrants to acquire Shares, (C) 24,951,596 Shares that can be obtained by Institutional Partners IIA upon the conversion of the Convertible Notes, (D) 2,592,856 Shares that can be obtained by Institutional
Partners IIA upon the conversion of the Bridge Notes and (E) 970,114 Shares that can be obtained by Institutional Partners IIA upon the conversion of the Reimbursement Notes.

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(vi) Institutional Advisors II may be deemed the beneficial owner of 67,004,089 Shares
(approximately 57.5% of the total number of Shares outstanding, calculated in accordance with Rule 13d-3(d)(1)(i) under the Act). This number consists of (A) (1) 3,240,750 Shares held for the account of Institutional Partners II,
(2) 4,479,892 Shares that can be obtained by Institutional Partners II upon the exercise of warrants to acquire Shares, (3) 9,904,157 Shares that can be obtained by Institutional Partners II upon the conversion of the Convertible Notes,
(4) 1,029,196 Shares that can be obtained by Institutional Partners II upon the conversion of the Bridge Notes and (5) 384,882 Shares that can be obtained by Institutional Partners II upon the conversion of the Reimbursement Notes, and
(B) (1) 8,164,436 Shares held for the account of Institutional Partners IIA, (2) 11,286,210 Shares that can be obtained by Institutional Partners IIA upon the exercise of warrants to acquire Shares, (3) 24,951,596 Shares that can
be obtained by Institutional Partners IIA upon the conversion of the Convertible Notes, (4) 2,592,856 Shares that can be obtained by Institutional Partners IIA upon the conversion of the Bridge Notes and (5) 970,114 Shares that can be
obtained by Institutional Partners IIA upon the conversion of the Reimbursement Notes.

(vii) MHRC may be deemed the
beneficial owner of 25,580,440 Shares (approximately 32.2% of the total number of Shares outstanding, calculated in accordance with Rule 13d-3(d)(1)(i) under the Act). This number consists of all of the Shares otherwise described in
Item 5(a)(iii) by virtue of MHRCs position as the managing member of Advisors.

(viii) MHRC II may be deemed the
beneficial owner of 67,004,089 Shares (approximately 57.5% of the total number of Shares outstanding, calculated in accordance with Rule 13d-3(d)(1)(i) under the Act). This number consists of all of the Shares otherwise described in
Item 5(a)(vi) by virtue of MHRC IIs position as the managing member of Institutional Advisors II.

(ix) Fund
Management may be deemed the beneficial owner of 92,584,529 Shares (approximately 68.6% of the total number of Shares outstanding, calculated in accordance with Rule 13d-3(d)(1)(i) under the Act). This number consists of all of the Shares otherwise
described in this Item 5(a) by virtue of Fund Managements investment management agreement with Master Account, Capital Partners (100), Institutional Partners II and Institutional Partners IIA.

(x) MHR Holdings may be deemed to be the beneficial owner of 92,584,529 Shares (approximately 68.6% of the total number of Shares
outstanding, calculated in accordance with Rule 13d-3(d)(1)(i) under the Act). This number consists of all of the Shares otherwise described in this Item 5(a) by virtue of MHR Holdings position as the managing member of Fund Management.

(xi) Dr. Rachesky may be deemed the beneficial owner of 93,073,827 Shares (approximately 68.7% of the total number of
Shares outstanding, calculated in accordance with Rule 13d-3(d)(1)(i) under the Act). This number consists of (A) all of the Shares otherwise described in this Item 5(a) by virtue of Dr. Racheskys position as the managing member
of each of MHRC, MHRC II and MHR Holdings, (B) 14,000 Shares that can be obtained upon the exercise of certain options to purchase Shares, (C) 470,000 Shares that can be obtained upon the exercise of certain non-qualified stock
options to purchase Shares and (D) 5,298 Shares held for his own account.

(b) (i) Master Account may be deemed to
have (x) the sole power to direct the disposition of 22,544,146 Shares which may be deemed to be beneficially owned by Master Account as described above, and (y) the sole power to direct the voting of 22,544,146 Shares which may be deemed
to be beneficially owned by Master Account as described above.

(ii) Capital Partners (100) may be deemed to have
(x) the sole power to direct the disposition of 3,036,294 Shares which may be deemed to be beneficially owned by Capital Partners (100) as described above, and (y) the sole power to direct the voting of 3,036,294 Shares which may be
deemed to be beneficially owned by Capital Partners (100) as described above.

(iii) Advisors may be deemed to have
(x) the sole power to direct the disposition of 25,580,440 Shares which may be deemed to be beneficially owned by Advisors as described above, and (y) the sole power to direct the voting of 25,580,440 Shares which may be deemed to be
beneficially owned by Advisors as described above.

(iv) Institutional Partners II may be deemed to have (x) the sole
power to direct the disposition of 19,038,877 Shares which may be deemed to be beneficially owned by Institutional Partners II as described above, and (y) the sole power to direct the voting of 19,038,877 Shares which may be deemed to be
beneficially owned by Institutional Partners II as described above.

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(v) Institutional Partners IIA may be deemed to have (x) the sole power to direct
the disposition of 47,965,212 Shares which may be deemed to be beneficially owned by Institutional Partners IIA as described above, and (y) the sole power to direct the voting of 47,965,212 Shares which may be deemed to be beneficially owned by
Institutional Partners IIA as described above.

(vi) Institutional Advisors II may be deemed to have (x) the sole power
to direct the disposition of 67,004,089 Shares which may be deemed to be beneficially owned by Institutional Advisors II as described above, and (y) the sole power to direct the voting of 67,004,089 Shares which may be deemed to be beneficially
owned by Institutional Advisors II as described above.

(vii) MHRC may be deemed to have (x) the sole power to direct the
disposition of the 25,580,440 Shares which may be deemed to be beneficially owned by MHRC as described above, and (y) the sole power to direct the voting of 25,580,440 Shares which may be deemed to be beneficially owned by MHRC as described
above.

(viii) MHRC II may be deemed to have (x) the sole power to direct the disposition of the 67,004,089 Shares which
may be deemed to be beneficially owned by MHRC II as described above, and (y) the sole power to direct the voting of 67,004,089 Shares which may be deemed to be beneficially owned by MHRC II as described above.

(ix) Fund Management may be deemed to have (x) the sole power to direct the disposition of the 92,584,529 Shares which may be deemed
to be beneficially owned by Fund Management as described above, and (y) the sole power to direct the voting of 92,584,529 Shares which may be deemed to be beneficially owned by Fund Management as described above.

(x) MHR Holdings may be deemed to have (x) the sole power to direct the disposition of 92,584,529 Shares which may be deemed to be
beneficially owned by MHR Holdings as described above, and (y) the sole power to direct the voting of 92,584,529 Shares which may be deemed to be beneficially owned by MHR Holdings as described above.

(xi) Dr. Rachesky may be deemed to have (x) the sole power to direct the disposition of the 97,073,827 Shares which may be
deemed to be beneficially owned by Dr. Rachesky as described above, and (y) the sole power to direct the voting of 97,073,827 Shares which may be deemed to be beneficially owned by Dr. Rachesky as described above.

(c) As reported on a Form 4 filed on July 5, 2017, on June 30, 2017, Master Account, Capital Partners (100), Institutional
Partners II and Institutional Partners IIA received additional Convertible Notes, Bridge Notes and Reimbursement Notes as paid-in-kind interest on the Convertible Notes, Bridge Notes and Reimbursement Notes already held by such Reporting Persons,
respectively. Such additional Convertible Notes are convertible into 569,855 Shares (in the case of Master Account), 77,928 Shares (in the case of Capital Partners (100)), 620,048 Shares (in the case of Institutional Partners II) and 1,562,092
Shares (in the case of Institutional Partners IIA). Such additional Bridge Notes are convertible into 84,766 Shares (in the case of Master Account), 11,276 Shares (in the case of Capital Partners (100)), 64,776 Shares (in the case of
Institutional Partners II) and 163,192 Shares (in the case of Institutional Partners IIA). Such additional Reimbursement Notes are convertible into 17,250 Shares (in the case of Master Account), 2,404 Shares (in the case of Capital
Partners (100)), 18,796 Shares (in the case of Institutional Partners II) and 47,376 Shares (in the case of Institutional Partners IIA). In addition, on May 18, 2017, Dr. Rachesky was granted 40,000 non-qualified stock options as
reported on a Form 4 filed on May 24, 2017.

(d) (i) The partners of Master Account, including Advisors, have the
right to participate in the receipt of dividends from, or proceeds from the sale of, the securities held for the account of Master Account in accordance with their partnership interests in Master Account.

(ii) The partners of Capital Partners (100), including Advisors, have the right to participate in the receipt of dividends from, or
proceeds from the sale of, the securities held for the account of Capital Partners (100) in accordance with their partnership interests in Capital Partners (100).

(iii) The partners of Institutional Partners II, including Institutional Advisors II, have the right to participate in the receipt of dividends from, or proceeds from the sale of, the securities held for
the account of Institutional Partners II in accordance with their partnership interests in Institutional Partners II.

(iv)
The partners of Institutional Partners IIA, including Institutional Advisors II, have the right to participate in the receipt of dividends from, or proceeds from the sale of, the securities held for the account of Institutional Partners IIA in
accordance with their partnership interests in Institutional Partners IIA.

(e) Not applicable.

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SIGNATURES

After reasonable inquiry and to the best of my knowledge and belief, the undersigned certifies that the information set forth in this
Statement is true, complete and correct.