Brother Elias had designed the lower basilica as an enormous
crypt with ribbed vaults. He had acquired his experience by building huge sepulchres out of hard rock in
Syria. The doors are surmounted by a large rose window, flanked by two smaller ones, called "the eye of the most beautiful church in the world" Martini also painted a
triptych depicting the
Madonna and Child with Two Hungarian Royal Saints with a row of five attendant saints in the St. Elizabeth Chapel (southern arm of the transept). These are among the greatest Martini's works and the finest examples of 14th-century painting. Over time, however, his use of
lead paint has led to the darkening of several sections of these works. . The other chapel on the left is dedicated to St.
Peter of Alcantara. The chapels on the right are dedicated to Saints: •
Louis of Toulouse and
Stephen I of Hungary, with frescoes by
Dono Doni (1575) and stained glass, attributed to Simone Martini. •
Anthony of Padua, with frescoes by
Cesare Sermei (1610). •
Mary Magdalene. This chapel, built by
Teobaldo Pontano (
the Bishop of Assisi from 1296 to 1329), contains some of the best works of the workshop of Giotto and maybe by the Master himself (about 1320). (It was wrongly attributed by
Vasari to
Puccio Capanna.) On the lateral walls are scenes from the
Life of Mary Magdalene (above the portrait of Teobaldo Pontano), while in the vault there are
roundels with busts of
Christ, the
Virgin,
Mary Magdalene and
Lazarus. The nave ends in a richly decorated semicircular
apse, preceded with a
transept with barrel vaulting. The frescoes in the right transept depict the childhood of Christ, partly by Giotto and his workshop and the
Nativity by the anonymous Maestro di San Nicola. The lowest level shows three frescoes representing St. Francis posthumously intervening in favour of two children. These frescoes by Giotto were revolutionary in their time, showing real people with emotions, set in a realistic landscape. with Saint Francis'', by
Cimabue. On the transept wall
Cimabue painted an image of
Our Lady enthroned and Saint Francis (1280). This is probably the nearest likeness existing, showing the actual appearance of Saint Francis. This static painting in Gothic style is in stark contrast with the lively frescoes of Giotto. This Chapel of
Saint Nicholas of Bari, at the northern end of the transept, was commissioned by the papal legate Cardinal
Napoleone Orsini and it contains the tomb of the cardinal's brother,
Giovanni Orsini, who died between 1292 and 1294. The
funerary monument is set in a niche above the altar, with the
recumbent effigy of a young man placed inside a mortuary chamber and flanked by two angels. The reliefs were carved by an Umbrian sculptor, probably of local origin. Between the tomb and the stained glass window appears a frescoed triptych attributed to Giotto's school, representing the Madonna and Child with Saint Francis and Nicholas. The cycle decorating the walls of the chapel, completed by 1307, comprises twelve scenes painted on the ceiling and on the walls illustrating the life and miracles of St Nicholas A scene of the chapel's dedication is painted above the arch of the entrance on the southern wall: the Redeemer receives the homage of Giovanni Orsini, presented by St. Nicholas, and of Napoleone Orsini, presented by Saint Francis. The stained glass windows show Cardinal Napoleone presented to Christ in the summit and his brother presented to Saint Nicholas in the zone below. At the southern end of the transept cardinal Orsini commissioned another chapel, dedicated to St John the Baptist, which was probably originally built for the tomb of Napoleone Orsini himself, but the cardinal was never buried there and the tomb remained empty. The parallel architectural arrangement of both Orsini chapels suggests that they were conceived together. However, the decorations of the chapel dedicated to Saint John the Baptist were never finished. Pietro Lorenzetti (or his workshop) executed a frescoed triptych with a
Madonna and Child with Saints John the Baptist and Francis. '' by
Pietro Lorenzetti on canvas. The left transept was decorated by the Sienese painter
Pietro Lorenzetti and his workshop between 1315 and 1330 (attributed by Vasari to Pietro Lorenzetti and also (wrongly) to Giotto and Puccio Capanna). This cycle of tempera frescoes are his masterworks. They depict six scenes from the
Passion of Christ. The fresco of
Deposition of the Cross is especially emotional. There were about 330 work-stages needed to complete this cycle. Beneath the monumental "Crucifixion" scene, Pietro Lorenzetti has executed a fresco of the Madonna and Child, accompanied by Saints
John the Evangelist and Saint Francis (the so-called
Madonna dei Tramonti). The fresco is accompanied by a frescoed niche containing the liturgical implements and a fictive bench. The juxtaposition of the
Childhood and the
Passion frescoes emphasizes the parallel between the
passion of Christ and the
compassion of St. Francis. The papal altar in the apse was made out of one block of stone from
Como in 1230. Around the altar are a series of ornamented Gothic arches, supported by columns in different styles. The fine Gothic walnut choir stalls were completed in 1471 by Apollonio Petrocchi da Ripatransone, with the help of Tommaso di Antonio Fiorentino and Andrea da Montefalco. Once featuring frescoes depicting an allegory of the Crucifixion by
Stefano Fiorentino (destroyed in 1622), the walls of the apse are now covered with a "Last Judgment" by
Cesare Sermei di Orvieto (1609–1668). The paintings in the lunettes of the vaults (1315–20) depict the
Triumph of St Francis and three allegories of
Obedience,
Poverty and
Chastity by the so-called
Maestro delle Vele (Master of the Assisi vaults), a pupil of Giotto (about 1330). The stained glass windows in this lower basilica are attributed to
Giovanni di Bonino and his workshop. ==Crypt==