On the last day of June 1944 she sortied for carrier strikes on the Bonins in support of the subsequent Marianas assault. Her planes scored well against aircraft on the ground and in the air as well as against gun installations, airfield and enemy ship ping. On 4 July strikes were launched against Iwo Jima, Chichi Jima and Ha Ha Jima with her planes battering the land, sinking a large cargo vessel in the harbor and firing three smaller ships.
On 6 July she began strikes on Guam and Rota to soften up for the invasion forces, and continued until the 21st when she lent direct support to enable safe landing of the first assault waves. Two days of replenishment at Saipan permitted her to steam i n TF 58 for photographic reconnaissance and air strikes against the islands of the Palau group. Her planes effected their mission on the 25th and 26th, exacting a heavy toll in enemy planes, ground installations, and shipping. She departed on 28 July en route to Saipan and the following day shifted to TG 68.1.
Although high seas prevented taking on needed bombs and rockets, Franklin steamed for another raid against the Bonins. The 4th of August bode well, for her fighters launched against Chichi Jima and her dive bombers and torpedo planes against a convoy north of Ototo Jima rained destruction against the radio stations, seaplane base, airstrips and ships.
A period of upkeep and recreation from 9 to 28 August ensued at Eniwetok before she departed in company with carriers Enterprise (CV-6), Belleau Wood (CVL-24) and San Jacinto (CVL-30) for neutralization and diversionary attacks against the Bonins. From 31 August to 2 September spirited and productive strikes from Franklin inflicted much ground damage, sank two cargo ships, bagged numerous enemy planes in flight, and accomplished photographic survey.
On 4 September she on loaded supplies at Saipan and steamed in TG 38.4 for an attack against Yap (3-6 September) which included direct air coverage of the Peleliu invasion on the 16th. The group took on supplies at Manus Island from 21-25 September.
Franklin as flagship of TG 38.4 returned to the Palau area where she launched daily patrols and night fighters. On 9 October she rendezvoused with carrier groups cooperating in air strikes in support of the coming occupation of Leyte. At twilight on the 13th, the Task Group came under attack by four bombers and Franklin twice was narrowly missed by torpedoes. An enemy plane crashed Franklin’s deck abaft the island structure, slid across the deck and into the water on her starboard beam.
Early on the 14th a fighter sweep was made against Aparri, Luzon, following which she steamed to the east of Luzon to neutralize installations to the east prior to invasion landings on Leyte. On the 16th she was attacked by three enemy planes, one of which scored with a bomb that hit the after outboard corner of the deck edge elevator, killing 3 and wounding 22. The tenacious carrier continued her daily operations hitting hard at Manila Bay on 19 October when her planes sank a number of ships, damaged many, destroyed a floating dry dock, and bagged 11 planes. 
During the initial landings on Leyte (20 October) her aircraft hit surrounding air strips, and launched search patrols in anticipation of the approach of a reported enemy attack force. On the morning of 24 October her planes sank a destroyer and damage d two others. Franklin, with Task Groups 38.4, 38.3, and 38.2 sped to intercept the advancing Japanese carrier force and attack at dawn. Franklin’s four strike groups combined with those from the other carriers in sending to the bottom four Japanese carriers, and battering their screens.
Retiring in her task group to refuel, she returned to the Leyte action on 27 October, her planes concentrating on a heavy cruiser and two destroyers south of Mindoro. She was underway about 1,000 miles off Samar on 30 October when enemy bombers appeared bent on a suicide mission. Three doggedly pursued Franklin, the first plummeting off her starboard side the second hitting the flight deck and crashing through to the gallery deck, showering destruction, killing 56 and wounding 60; the third disc harging another near miss at Franklin before diving into the flight deck of Belleau Wood.
Both carriers retired to Ulithi for temporary repairs and Franklin proceeded to Puget Sound Navy Yard arriving 28 November 1944 for battle damage overhaul.
She departed Bremerton on 2 February 1945 and after training exercises and pilot qualification joined TG 58.2 for strikes on the Japanese homeland in support of the Okinawa landings. On 15 March she rendezvoused with TF 58 units and 3 days later launch ed sweeps and strikes against Kagoshima and Izumi on southern Kyushu.
Before dawn on 19 March 1945 Franklin who had maneuvered closer to the Japanese mainland than had any other U.S. carrier during the war, launched a fighter sweep against Honshu and later a strike against shipping in Kobe Harbor. Suddenly, a single enemy plane pierced the cloud cover and made a low level run on the gallant ship to drop two semi-armor piercing bombs. One struck the flight deck centerline, penetrating to the hangar deck, effecting destruction and igniting fires through the second and third decks, and knocking out the combat information center and airplot. The second hit aft, tearing through two decks and fanning fires which triggered ammunition, bombs and rockets. Franklin, within 50 miles of the Japanese mainland, lay dead in the water, took a 13° starboard list, lost all radio communications, and broiled under the heat from nveloping fires. Many of the crew were blown overboard, driven off by fire, killed or wounded, but the 106 officers and 604 enlisted who voluntarily remained saved their ship through sheer valor and tenacity. The casualties totaled 724 killed and 265 wounded, and would have far exceeded this number except for the heroic work of many survivors. Among these were Medal of Honor winners, Lieutenant Commander Joseph T. O’Callahan, S. J., USNR, the ship’s chaplain, who administered the last rites organized and directed firefighting and rescue parties and led men below to wet down magazines that threatened to explode, and Lieutenant (junior grade) Donald Gary who discovered 300 men trapped in a blackened mess compartment, and finding an exit returned repeatedly to lead groups to safety. Santa Fe (CL-60) similarly rendered vital assistance in rescuing crewmen from the sea and closing Franklin to take off the numerous wounded.